diff --git a/DESCRIPTION b/DESCRIPTION
index ee2b32c..c66c6be 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,4 +1,4 @@
-Package: TAPACLOTH
+Package: INCOMMON
 Title: Targeted panel-oriented test for clonality and heterozygosity
 Version: 0.0.1
 Author: Nicola Calonaci
@@ -8,15 +8,16 @@ Authors@R:
            comment = c(ORCID = "0000-0003-2721-4888")),
     person("Giulio", "Caravagna", , "gcaravag@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "")))
-Description: TAPACLOTH is a tool that classifies somatic mutation calls from
-    targeted-panel sequencing as either subclonal, clonal heterozygous or clonal 
-    LOH thorugh a statistical hypothesis test based on a Binomial or Beta-Binomial 
-    modelling of the sequencing read count process. As an additional feature, 
-    TAPACLOTH can be used to infer sample purity.
+Description: INCOMMON is a tool for the INference of COpy number and Mutation Multiplicity in ONcology. 
+            INCOMMON infers the copy number and multiplicity of somatic mutations from tumour-only read count data, 
+            and can be applied to classify mutations from large-size datasets in an efficient and fast way.
+            Mutations are classified as either Tier-1 (present in 100% cells) without copy-number alterations 
+            (heterozygous mutant diploid HMD), with loss of heterozygosity (LOH), copy-neutral LOH (CNLOH), amplification (AM), 
+            or Tier-2 (subclonal or with high ploidy and low multiplicity).
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.1
 Suggests: 
     knitr,
     rmarkdown,
@@ -36,8 +37,8 @@ Imports:
 Remotes:
     caravagnalab/BMix,
     caravagnalab/CNAqc
-URL: https://github.com/caravagnalab/TAPACLOTH
-BugReports: https://github.com/caravagnalab/TAPACLOTH/issues
+URL: https://github.com/caravagnalab/INCOMMON
+BugReports: https://github.com/caravagnalab/INCOMMON/issues
 VignetteBuilder: knitr
 Depends: 
     R (>= 2.10)
diff --git a/LICENSE b/LICENSE
index eca47de..30b1978 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,2 +1,2 @@
 YEAR: 2022
-COPYRIGHT HOLDER: TAPACLOTH authors
+COPYRIGHT HOLDER: INCOMMON authors
diff --git a/NAMESPACE b/NAMESPACE
index 4a1376a..596a1fa 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,41 +1,23 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(print,TAPACLOTH)
-export(binomial_test)
-export(estimate_purity)
-export(gene_label)
-export(gene_entropy)
-export(get_DP)
-export(get_NV)
-export(get_VAF)
-export(get_classes)
-export(get_classifier)
-export(get_coord)
-export(get_gene)
-export(get_id)
-export(get_params)
-export(get_purity_bmix)
-export(get_purity_estimate)
-export(get_reliability)
+S3method(plot,INCOMMON)
+S3method(print,INCOMMON)
+export(classification)
+export(classify)
+export(compute_posterior)
 export(init)
-export(models_avail)
-export(plot.TAPACLOTH)
-export(plot_bmix)
+export(parameters)
+export(plot_classification)
 export(plot_gene)
-export(plot_heatmap)
 export(plot_summary)
-export(plot_test)
-export(run_classifier)
-export(test_setup)
+export(posterior)
 import(CNAqc)
-import(VGAM)
 import(cli)
 import(crayon)
 import(ggplot2)
 import(ggridges)
 import(ggsci)
 import(pheatmap)
-import(stringr)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,filter)
 importFrom(dplyr,mutate)
diff --git a/R/binomial_test.R b/R/binomial_test.R
deleted file mode 100644
index c5c5227..0000000
--- a/R/binomial_test.R
+++ /dev/null
@@ -1,183 +0,0 @@
-#' Compute likelihoods and uncertainty..
-#'
-#' @param test Number of reads with the variant.
-#' @param DP Sequencing coverage of the mutated genome site.
-#' @param purity Purity of the sample.
-#' @param cutoff Likelihood cut-off for class assignment.
-#' @param model Model used for the classification task, either "Binomial" (no over-dispersion) 
-#' or "Beta-Binomial" (over-dispersion included), that will be used as the expected 
-#' distribution for the number of reads with variant at fixed coverage and purity.
-#' @param rho If "Beta-Binomial" model is selected, this parameter tunes the over-dispersion
-#' of the expected distribution used for the classification.
-#' @param karyotypes Karyotypes to be included among the possible classes.
-#' @return A tibble including ploidy, multiplicity, proportion of wt alleles, 
-#' uncertainty  of the class assignment, model density.
-#' @export
-#' @importFrom dplyr filter mutate rename select %>% 
-#' @examples
-#' binomial_test(test = 220,
-#' DP = 500,
-#' purity = 0.98,
-#' cutoff = 0.9,
-#' model = "Beta-Binomial",
-#' rho = 0.01,
-#' karyotypes = c("1:0","1:1","2:0","2:1","2:2")
-#')
-
-binomial_test = function(test,
-                         DP,
-                         gene,
-                         priors = "NULL",
-                         purity,
-                         cutoff,
-                         rho = 0.01,
-                         karyotypes,
-                         assign_extremes
-                         )
-{
-  NV_x = 1:DP
-  
-  # Density
-  db = function(Major, minor, priors, gene)
-  {
-    peaks = CNAqc:::expected_vaf_peak(Major, minor, purity)$peak
-    
-    lapply(peaks %>% seq_along, function(p) {
-      label = paste0(Major + minor, 'N (Mutated: ', p, "N)")
-      
-      out = data.frame(
-        density = compute_density(NV_x, DP, prob = peaks[p], rho),
-        NV = NV_x,
-        Major = Major,
-        minor = minor,
-        ploidy = Major + minor,
-        multiplicity = p,
-        karyotype = paste0(Major, ":", minor),
-        label = label,
-        peak = peaks[p]
-      )
-      
-      if (!is.null(priors))
-        out$density = out$density * get_prior(priors, gene, label)
-      
-      out
-      
-    }) %>%
-      Reduce(f = bind_rows)
-  }
-  
-  cut = function(x, cutoff)
-  {
-   
-    ## Normalize likelihoods by maximum and compute corresponding cut-offs 
-    x = x %>% 
-      group_by(label) %>% 
-      reframe(
-        density,
-        NV,
-        ploidy,
-        multiplicity,
-        label,
-        peak,
-        cutoff = max(density) * cutoff
-      ) %>% 
-      unique() %>% 
-      ungroup()
-    
-    ## Compute assignment probability (relative likelihood) for each class
-      
-    x = x %>% 
-      group_by(NV) %>% 
-      reframe(
-        density,
-        ploidy,
-        multiplicity,
-        peak,
-        cutoff,
-        label,
-        p_assign = density / sum(density),
-        entropy = 1 - (density / sum(density))
-        # entropy = 1 - max(density) / sum(density)
-      ) %>% 
-      ungroup()
-    
-    ## Add out-of-sample label for densities lower than cut-offs
-    x = x %>% 
-      mutate(label = ifelse(density < cutoff, "out of sample", label))
-    x
-  }
-  
-  if(is.na(purity)){
-    cli_alert_warning(text = 
-                        "With purity {.field {purity}} classification is not possible."
-    )
-    return(tibble(ploidy = NA,
-                  multiplicity = NA,
-                  entropy = NA,
-                  label = NA,
-                  density = list(NULL)))
-  }
-  
-  dataset = lapply(karyotypes, function(k) {
-    alleles = strsplit(k, split = ":")[[1]] %>% as.integer()
-    db(alleles[1],alleles[2], priors, gene)
-  }) %>% bind_rows() %>% cut(cutoff)
-  
-  # Compute mean entropy over in-sample data
-  
-  mean_entropy = dataset %>% 
-    filter(label != "out of sample") %>% 
-    group_by(NV) %>% 
-    summarise(u = min(entropy)) %>% 
-    pull(u) %>% 
-    mean()
-  
-  
-  tested = dataset %>%
-    maximise() %>%
-    dplyr::filter(NV == test)
-  
-  if(nrow(tested)>1){
-    cli_alert_warning(text = 
-                        "With purity {.field {purity}} classes {.field {tested$label}} have the same likelihood"
-                      )
-    cli_alert_warning(text = 
-                        "Simplest case will be selected: {.field {tested$label[1]}}"
-    )
-    
-    tested = tested[1.,]
-  }
-
-    # Optionally assign NVs lower than minimum (larger than maximum) accepted to 
-  # Subclonal/Higher Ploidy (Higher Ploidy and Multiplicity)
-  if(tested$label == "out of sample" & assign_extremes){
-    min_in_sample = dataset %>%
-      dplyr::filter(label != "out of sample") %>%
-      dplyr::filter(NV == min(NV)) %>%
-      pull(NV) %>% unique()
-    
-    max_in_sample = dataset %>%
-      dplyr::filter(label != "out of sample") %>%
-      dplyr::filter(NV == max(NV)) %>%
-      pull(NV) %>% unique()
-    
-    # tested$label = ifelse(tested$NV < min_in_sample | tested$NV > max_in_sample,
-    #                       paste0(tested$ploidy,'N (Mutated: ', tested$multiplicity,"N)"),
-    #                       tested$label)
-    # tested$label = ifelse(tested$NV < min_in_sample | tested$NV > max_in_sample,
-    #                       paste0(tested$ploidy,'N (Mutated: ', tested$multiplicity,"N)"),
-    #                       tested$label)
-    if(tested$NV < min_in_sample) tested$label = "SUB/HPLM"
-    if(tested$NV > max_in_sample) tested$label = "HPHM"
-  }
-  
-  
-  return(tibble(ploidy = tested$ploidy,
-                multiplicity = tested$multiplicity,
-                p_assign = tested$p_assign,
-                entropy = tested$entropy,
-                label = tested$label,
-                density = list(dataset),
-                mean_entropy = mean_entropy))
-}
-  
\ No newline at end of file
diff --git a/R/classes.R b/R/classes.R
deleted file mode 100644
index d970cc3..0000000
--- a/R/classes.R
+++ /dev/null
@@ -1,29 +0,0 @@
-classes = function(x, model = "binomial") {
-  stopifnot(inherits(x, "TAPACLOTH"))
-  if ((model %>% tolower()) %in% c("binomial", "beta-binomial", "terzile"))
-  {
-    x$data$data %>%
-      cbind(x$classifier[[model]]$data) %>%
-      as_tibble() %>%
-      print()
-  }
-  else{
-    cli::cli_alert("No classification using model {.format {model}}")
-  }
-}
-
-purity_per_sample = function(x) {
-  stopifnot(inherits(x, "TAPACLOTH"))
-  
-  for (model in x$purity_estimate %>% names()) {
-    if ((model %>% tolower()) %in% c("binomial", "beta-binomial"))
-    {
-      x$data$purity %>%
-        dplyr::rename(input_purity = purity) %>%
-        full_join(x$purity_estimate[[model]]$reliability, by = "sample") %>%
-        full_join(x$purity_estimate[[model]]$purity, by = "sample") %>%
-        print()
-    }
-    
-  }
-}
\ No newline at end of file
diff --git a/R/classify.R b/R/classify.R
new file mode 100644
index 0000000..cc834d8
--- /dev/null
+++ b/R/classify.R
@@ -0,0 +1,116 @@
+#' Classify mutations using a Beta-Binomial model-based test.
+#'
+#' @param x An object of class \code{'INCOMMON'} generated with function `init`.
+#' @param priors 
+#' @param entropy_cutoff Entropy cut-off for Tier-1 vs Tier-2 assignment.
+#' @param rho Over-dispersion parameter.
+#' @param karyotypes Karyotypes to be included among the possible classes.
+#' @return An object of class `INCOMMON` containing the original input plus
+#' the classification data and parameters.
+#' @export
+#' @importFrom dplyr filter mutate rename select %>% 
+#' @examples
+#' x = init(mutations = example_data$data,
+#'          sample = example_data$sample,
+#'          purity = example_data$purity,
+#'          tumor_type = example_data$tumor_type)
+#' x = classify(
+#'     x = x, 
+#'     priors = priors,
+#'     entropy_cutoff = 0.2,
+#'     rho = 0.01,
+#'     karyotypes = c("1:0","1:1","2:0","2:1","2:2")
+#'     )
+#' print(x)
+classify = function(x,
+                    priors = NULL,
+                    entropy_cutoff = 0.2,
+                    rho = 0.01,
+                    karyotypes = c("1:0", "1:1", "2:0", "2:1", "2:2")
+                    
+)
+  {
+  stopifnot(inherits(x, "INCOMMON"))
+  if(is.null(entropy_cutoff)) entropy_cutoff = 1
+  
+  # Output
+  
+  output = x
+  
+  if (!("fit" %in% names(output)))
+    output$fit = list()
+  
+  cli::cli_h1(
+      "INCOMMON inference of copy number and mutation multiplicity for sample {.field {x$sample}}"
+    )
+    cat("\n")
+    
+  check_input(x)
+    
+  cli::cli_alert_info("Performing classification")
+    
+  x = idify(x)
+    
+  tests = lapply(ids(x), function(id) {
+    # Control for duplicates
+    if(info(x, mutation_id = id) %>% nrow() > 1){
+      cli_alert_warning(text = "More than one mutation mapped at: {.field {id}}")
+      info(x, id)
+      
+      cli_alert_warning(text = "Keeping first row by default (check your input data)")
+      w = which(data(x)$id==id)
+      x$data = x$data[-w[2:length(w)],]
+    }
+    
+    # Compute model likelihood, posterior and entropy
+    
+    compute_posterior(
+      NV = NV(x, id),
+      DP = DP(x, id),
+      gene = gene(x, id),
+      priors = priors,
+      tumor_type = tumor_type(x),
+      purity = purity(x),
+      entropy_cutoff = entropy_cutoff,
+      rho = rho,
+      karyotypes = karyotypes,
+    )
+  })
+  
+  names(tests) = ids(x)
+  
+  # Maximum a posteriori classification
+  map_estimates = lapply(ids(x), function(id){
+    
+    map = tests[[id]] %>% 
+      dplyr::group_by(NV) %>% 
+      dplyr::filter(value == max(value)) %>% 
+      dplyr::filter(NV == NV(x, id)) %>% 
+      dplyr::ungroup()
+
+    if(nrow(map)>1){
+      cli_alert_warning(text =
+                          "With purity {.field {purity(x)}} karyotype {.field {map$karyotype}} with multiplicities {.field {map$multiplicity}} have the same likelihood"
+                        )
+      cli_alert_warning(text =
+                          "Simplest case will be selected: {.field {map$karyotype[1]}}"
+      )
+
+      map = map[1.,]
+    }
+    
+    map %>% dplyr::select(label, state, value, entropy) %>% dplyr::rename(posterior = value)
+}) %>% do.call(rbind, .)
+  
+  # Add fit object
+    output$fit = list(
+      classification = dplyr::bind_cols(data(x), map_estimates),
+      params = tibble(entropy_cutoff = entropy_cutoff,
+                      rho = rho),
+      posterior = tests
+    )
+    
+  return(output)
+}
+
+
diff --git a/R/compute_density.R b/R/compute_likelihood.R
similarity index 65%
rename from R/compute_density.R
rename to R/compute_likelihood.R
index da8d54d..3a689be 100644
--- a/R/compute_density.R
+++ b/R/compute_likelihood.R
@@ -1,4 +1,4 @@
-compute_density = function(NV, DP, prob, rho) {
+compute_likelihood = function(NV, DP, prob, rho) {
   density = VGAM::dbetabinom(
     x = 1:DP,
     size = DP,
diff --git a/R/compute_posterior.R b/R/compute_posterior.R
new file mode 100644
index 0000000..79a2d00
--- /dev/null
+++ b/R/compute_posterior.R
@@ -0,0 +1,138 @@
+#' Compute model likelihood, posterior and entropy
+#'
+#' @param NV Number of reads with the variant.
+#' @param DP Sequencing coverage of the mutated genome site.
+#' @param gene Gene name or symbol.
+#' @param priors Prior distribution.
+#' @param purity Purity of the sample.
+#' @param tumor_type Tumor type of the sample.
+#' @param entropy_cutoff Cut-off on entropy for Tier-1/Tier-2 distinction.
+#' @param model Model used for the classification task, either "Binomial" (no over-dispersion) 
+#' or "Beta-Binomial" (over-dispersion included), that will be used as the expected 
+#' distribution for the number of reads with variant at fixed coverage and purity.
+#' @param rho If "Beta-Binomial" model is selected, this parameter tunes the over-dispersion
+#' of the expected distribution used for the classification.
+#' @param karyotypes Karyotypes to be included among the possible classes.
+#' @return A tibble including ploidy, multiplicity, proportion of wt alleles, 
+#' uncertainty  of the class assignment, model density.
+#' @export
+#' @importFrom dplyr filter mutate rename select %>% 
+#' @examples
+#' binomial_test(test = 220,
+#' DP = 500,
+#' purity = 0.98,
+#' cutoff = 0.9,
+#' model = "Beta-Binomial",
+#' rho = 0.01,
+#' karyotypes = c("1:0","1:1","2:0","2:1","2:2")
+#')
+
+compute_posterior = function(NV,
+                         DP,
+                         gene,
+                         priors = NULL,
+                         tumor_type,
+                         purity,
+                         entropy_cutoff,
+                         rho = 0.01,
+                         karyotypes,
+                         assign_extremes
+                         )
+{
+  NV_x = 1:DP
+  
+  # Density
+  db = function(Major, minor, prior, gene)
+  {
+    
+    expected_peaks = CNAqc:::expected_vaf_peak(Major, minor, purity)$peak
+    
+    lapply(expected_peaks %>% seq_along(), function(p) {
+      
+      # Classification label
+      label = paste0(Major + minor, 'N (Mutated: ', p, "N)")
+      
+      if(!(label %in% priors$label)) cli::cli_alert_danger("Incomplete prior distribution!")
+      stopifnot(label %in% priors$label)
+      prior = prior %>% dplyr::filter(label == !!label) %>% dplyr::pull(p)
+      
+      # Expected VAF peak of mixture component
+      expected_peak = expected_peaks[p]
+      
+      # Beta-Binomial likelihood distribution
+      likelihood = compute_likelihood(NV = NV_x, DP = DP, prob = expected_peak, rho = rho)
+      
+      # # Posterior distribution
+      # if (is.null(priors)){
+      #   prior = 1
+      # } else {
+      #   prior = get_prior(priors, gene, tumor_type, label)
+      # }
+      
+      posterior = prior*likelihood
+      posterior = posterior/sum(posterior) # Normalise
+      
+      # Output
+      out = data.frame(
+        value = posterior,
+        NV = NV_x,
+        Major = Major,
+        minor = minor,
+        ploidy = Major + minor,
+        multiplicity = p,
+        karyotype = paste0(Major, ":", minor),
+        label = label,
+        peak = expected_peak
+      )
+      
+      out
+      
+    }) %>%
+      do.call(bind_rows, .)
+  }
+  
+  if(is.na(purity)){
+    cli_alert_warning(text = 
+                        "With purity {.field {purity}} classification is not possible."
+    )
+    return(tibble(ploidy = NA,
+                  multiplicity = NA,
+                  entropy = NA,
+                  label = NA,
+                  density = list(NULL)))
+  }
+  
+  # Compute posterior distribution of 0 < NV <= DP for each component of the mixture (karyotype)
+  # Prior distribution
+  if (is.null(priors)){
+    prior = 1
+  } else {
+    prior = get_prior(priors, gene, tumor_type)
+  }
+  posterior = lapply(karyotypes, function(k) {
+    alleles = strsplit(k, split = ":")[[1]] %>% as.integer()
+    db(Major = alleles[1], 
+       minor = alleles[2], 
+       prior =  prior, 
+       gene = gene)
+  }) %>% 
+    bind_rows()
+  
+  # Compute entropy
+  posterior = posterior %>% 
+    dplyr::group_by(NV) %>% 
+    dplyr::reframe(value, NV, Major, minor, ploidy, multiplicity, karyotype, label, peak, entropy = -sum(value*log2(value)))
+  
+  # Apply entropy cutoff
+  posterior = posterior %>% 
+    dplyr::mutate(state = dplyr::case_when(
+      label %in% c('4N (Mutated: 1N)', '3N (Mutated: 1N)') | entropy > entropy_cutoff ~ 'Tier-2',
+      entropy <= entropy_cutoff & label %in% c("2N (Mutated: 1N)") ~ "HMD",
+      entropy <= entropy_cutoff & label %in% c("1N (Mutated: 1N)") ~ "LOH",
+      entropy <= entropy_cutoff & label %in% c("2N (Mutated: 2N)") ~ "CNLOH",
+      entropy <= entropy_cutoff & label %in% c("3N (Mutated: 2N)", "4N (Mutated: 2N)") ~ "AM"
+    ))
+  
+  return(posterior)
+}
+  
\ No newline at end of file
diff --git a/R/estimate_purity.R b/R/estimate_purity.R
deleted file mode 100644
index 8bd7a57..0000000
--- a/R/estimate_purity.R
+++ /dev/null
@@ -1,62 +0,0 @@
-#' Infer sample purity using a mixture of Binomial or Beta-Binomial distributions.
-#'
-#' @param x An object of class \code{'TAPACLOTH'} generated with function `init`.
-#' @param eps In case data is fitted with a mixture of 2 distributions, sample purity
-#' is estimated using only that whose peak is closer to the input purity estimate
-#' than the value of this parameter. If both distributions satisfy this condition,
-#' the one which is closest to the input purity estimate is used for the new estimate.
-#'
-#' @return An object of class `TAPACLOTH` containing the inferred purity.
-#' @export
-#'
-#' @examples
-#' input = init(mutations = example_data$data, sample = example_data$sample, purity = example_data$purity)
-#' out = estimate_purity(x = input, model = "binomial", eps = 0.01)
-#' print(out)
-estimate_purity = function(x,
-                           eps = 0.01) 
-  {
-  
-  stopifnot(inherits(x, "TAPACLOTH"))
-  
-  # Output
-  test = x
-  if (!("purity_estimate" %in% names(test)))
-    test$purity_estimate = list()
-  
-  cli::cli_h1(
-    "TAPACLOTH purity estimate of sample {.field {get_sample(x)}} using a Beta-binomial model"
-  )
-  cat("\n")
-  
-  # Prepare data for BMix
-  input = data.frame(successes = get_data(x) %>% pull(NV),
-                     trials = get_data(x) %>% pull(DP))
-  # Return NA if NVs are less than 3
-  if (nrow(input) <= 3) {
-    cli::cli_alert("There are less than 4 SNVs: purity will not be estimated")
-    return(test)
-  }
-  
-  fit = BMix::bmixfit(input, K.Binomials = 0, K.BetaBinomials = 1:3)
-  n_binomials = fit$K["BB"]
-  peaks = sort(fit$BB.params["mu",]) %>% as.double()
-  purity_bmix = purity_from_fit(
-    n_binomials = n_binomials,
-    peaks = peaks,
-    purity = get_purity(x),
-    eps = eps
-  )
-  plot_bmix = BMix::plot.bmix(fit, input)
-  
-  # Prepare output
-  fit$data = input
-  fit$plot_bmix = BMix::plot.bmix(fit, fit$data)
-  fit$eps = eps
-  fit$purity = min(purity_bmix, 1) %>% round(2)
-  fit$reliability = ifelse(get_purity(x) == 0.0, NA, 1-sqrt(((get_purity(x)-fit$purity)/fit$purity)**2))
-  
-  test$purity_estimate = fit
-  
-  return(test)
-}
diff --git a/R/init.R b/R/init.R
index f0937b0..2b1054a 100644
--- a/R/init.R
+++ b/R/init.R
@@ -6,22 +6,24 @@
 #'   reference allel `ref`, alternative allele `alt`, integer sequencing depth `DP`, integer number
 #'   of reads with variant `NV`, variant allelic frequency `VAF` and gene name `gene`
 #'   as Hugo Symbol.
-#' @param sample Sample name.
-#' @param purity Sample purity.
+#' @param sample Sample name or ID.
+#' @param tumor_type Tumor type of the sample.
+#' @param purity Purity of the sample.
 #' @param gene_roles A tibble reporting a list of `gene` names and associated
 #'  `gene_role` among "oncogene", "TSG" and "fusion". The default is taken from COSMIC Cancer Gene Census.
-#' @return An object of class \code{TAPACLOTH}.
+#' @return An object of class \code{INCOMMON}.
 #' @export
 #' @examples 
-#' input = init(mutations = example_data$data, sample = example_data$sample, purity = example_data$purity)
+#' input = init(mutations = example_data$data, sample = example_data$sample, purity = example_data$purity, tumor_type = example_data$tumor_type)
 #' print(input)
-init = function(mutations, sample, purity, gene_roles = TAPACLOTH::cancer_gene_census){
+init = function(mutations, sample, tumor_type, purity, gene_roles = INCOMMON::cancer_gene_census){
   mutations = dplyr::left_join(mutations, gene_roles, by = "gene")
   out = list(
     data = mutations,
     sample = sample,
-    purity = purity
+    purity = purity,
+    tumor_type = tumor_type
   )
-  class(out) = "TAPACLOTH"
+  class(out) = "INCOMMON"
   return(out)
 }
diff --git a/R/plot_classification.R b/R/plot_classification.R
new file mode 100644
index 0000000..ac7f96d
--- /dev/null
+++ b/R/plot_classification.R
@@ -0,0 +1,99 @@
+#' Visualize classification results for individual observations.
+#'
+#' @param x An object of class \code{'INCOMMON'} containing the classification results, as 
+#' produced by function `classify`.
+#' @return An object or a list of objects of class \code{'ggplot2'}.
+#' @export
+#' @importFrom dplyr filter mutate rename select %>% 
+#' @examples
+#' x = init(mutations = example_data$data,
+#'          sample = example_data$sample,
+#'          purity = example_data$purity,
+#'          tumor_type = example_data$tumor_type)
+#' x = classify(
+#'     x = x, 
+#'     priors = priors,
+#'     entropy_cutoff = 0.2,
+#'     rho = 0.01,
+#'     karyotypes = c("1:0","1:1","2:0","2:1","2:2")
+#'     )
+#' plot_test(x = x, id = ids(x)[1])
+plot_classification = function(x, assembly = F){
+  
+  stopifnot(inherits(x,"INCOMMON"))
+  
+  plots = lapply(ids(x), function(id){
+    
+    # Get posterior of specific classified mutations in easy-to-plot format
+    toplot = posterior(x, id = id)
+    toplot = toplot %>% dplyr::group_by(NV) %>% dplyr::reframe(max = (value == max(value)), dplyr::across(dplyr::everything()))
+      
+    toplot$multiplicity = factor(toplot$multiplicity)
+    toplot$ploidy = factor(toplot$ploidy)
+    
+    highlight = toplot %>% dplyr::filter(max)
+    highlight = lapply(split(highlight, highlight$label), function(s){ 
+      if(nrow(s) >= 20){
+        stride = as.integer(nrow(s)/20)
+        s = s[seq(1,nrow(s),stride),]
+      }
+      s
+    }) %>% do.call(rbind, .)
+    
+    # Get scale factor for overlapped visualisation of posterior and entropy
+    scaleFactor = max(toplot$value)/max(toplot$entropy)
+    scaleFactor = ifelse(is.infinite(scaleFactor), 1, scaleFactor)
+    
+    plot = toplot %>% 
+      ggplot() +
+      geom_line(aes(x = NV, y = value), 
+                color = 'white',  
+                size = .5, 
+                alpha = 0)+
+      geom_line(
+        aes(x = NV, y = entropy * scaleFactor),
+        color = "deeppink4",
+        size = 0.5,
+        linetype = "longdash",
+        alpha = .4
+      ) +
+      geom_point(data = highlight,
+                 aes(x = NV,
+                     y = value,
+                     color = ploidy,
+                     shape = multiplicity
+                 ),
+                 size = 1) +
+      geom_line(data = highlight,
+                 aes(x = NV,
+                     y = value,
+                     color = ploidy,
+                     group = label
+                 ),
+                 size = .5) +
+      geom_vline(
+        xintercept = NV(x, id),
+        color = 'black',
+        linetype = 'dashed',
+        size = .5
+      )+
+      scale_size_manual(values = c("1"=.3,"2"=.3))+
+      scale_y_continuous("Classification Probability", 
+                         sec.axis = sec_axis(~./scaleFactor, name = "Classification Entropy"), 
+                         limits = c(0,max(toplot$value)))+
+      scale_color_manual(values = ploidy_colors)+
+      CNAqc:::my_ggplot_theme() +
+      theme(axis.title.y.right = element_text(color="deeppink4"),
+            axis.text.y.right = element_text(color="deeppink4"))+
+      guides(size = "none",
+             shape = guide_legend(title = 'Multiplicity', ncol = 1),
+             color = guide_legend(title = 'Ploidy', ncol = 2))+
+      labs(title = paste0(info(x, id)$gene, ' (', info(x, id)$state, ')'),
+           subtitle = paste0(x$sample, ' (Purity = ', purity(x), '); ', info(x, id)$chr, '; ', info(x, id)$from, '; ', info(x, id)$ref, '>', info(x, id)$alt),
+           caption = paste0('Entropy cut-off: ', parameters(x)$entropy_cutoff, '; Overdispersion: ', parameters(x)$rho))
+      
+  })
+  if(assembly){
+    ggpubr::ggarrange(plotlist = plots, ncol = 4)
+  } else plots
+}
\ No newline at end of file
diff --git a/R/plot_fit.R b/R/plot_fit.R
deleted file mode 100644
index f646d0f..0000000
--- a/R/plot_fit.R
+++ /dev/null
@@ -1,65 +0,0 @@
-plot_fit = function(x, target_gene, sample_name, model) {
-  # if(x$classifier$model == "terzile") {
-  #   x$data = x$data %>%
-  #     dplyr::mutate(class = class_terzile)
-  # } else {
-  #   x$data = x$data %>%
-  #     dplyr::mutate(class = class_binom)
-  # }
-
-  # Select sample
-  data = x$data$data %>%
-    cbind(x$classifier[[model]]$data) %>%
-    dplyr::filter(sample == sample_name)
-
-  # Get class of mutations on target gene
-  gene_status = data %>%
-    dplyr::filter(gene == target_gene) %>%
-    dplyr::mutate(class = paste0(class, ' (', nv, '/', dp, ')')) %>%
-    dplyr::pull(class) %>%
-    paste(collapse = ', ')
-
-  # Get VAF of mutations on target gene
-  gene_vafs = data %>%
-    dplyr::filter(gene == target_gene) %>%
-    dplyr::pull(VAF)
-
-  # Fit plot
-  colormap = ggsci::pal_jama("default")(7)[1:3]
-  names(colormap) = c("Clonal", "Clonal LOH", "Subclonal")
-  fit_plot = data %>%
-    ggplot2::ggplot() +
-    CNAqc:::my_ggplot_theme() +
-    ggplot2::geom_histogram(binwidth = 0.01, aes(VAF, fill = class)) +
-    ggplot2::scale_fill_manual(values = colormap)+
-    # ggsci::scale_fill_jama() +
-    xlim(0, 1) +
-    ggplot2::labs(
-      title = sample_name,
-      subtitle = paste0("Purity: ", filter(x$data$purity, sample == sample_name)$purity, " - ", target_gene, ": ", gene_status)
-    ) +
-    ggplot2::guides(fill = guide_legend(''),
-           color = guide_legend('', override.aes = aes(fill = NA)))  +
-    ggplot2::geom_vline(aes(xintercept = gene_vafs,
-                   color = "Target VAF"),
-               linetype = 6) +
-    ggplot2::geom_vline(
-      aes(xintercept = filter(x$data$purity, sample == sample_name)$purity,
-          color = "Purity"),
-      linetype = 'dashed',
-      size = .6
-    ) +
-    ggplot2::geom_vline(aes(xintercept = filter(x$data$purity, sample == sample_name)$purity / 2,
-                   color = "Clonal peak"),
-               linetype = 'dashed') +
-    ggplot2::scale_color_manual(
-      name = "",
-      values = c(
-        `Target VAF` = "indianred3",
-        `Purity` = "black",
-        `Clonal Peak` = "gray"
-      )
-    )
-
-  return(fit_plot)
-}
\ No newline at end of file
diff --git a/R/plot_heatmap.R b/R/plot_heatmap.R
deleted file mode 100644
index 1d1ba54..0000000
--- a/R/plot_heatmap.R
+++ /dev/null
@@ -1,159 +0,0 @@
-#'Plotting function for class \code{'TAPACLOTH'}.
-#' @description
-#' Generates a composite heatmap with useful information on data and classification results.
-#' @param x An obj of class \code{'TAPACLOTH'} containing a `classifier`.
-#' @param model Model used for the test, either "Binomial" or "Beta-Binomial".
-#' @import pheatmap
-#' @import CNAqc
-#' @import ggplot2
-#' @import ggsci 
-#' @import ggridges 
-#' @importFrom dplyr filter mutate rename select %>% 
-#' @return An object of class \code{'TAPACLOTH'} containing a list of ggplot2
-#' plots named `plot_test` inside `classifier`.
-#' @export
-#' @examples
-#' x = init(mutations = example_data$data, sample = example_data$sample, purity = example_data$purity)
-#' x = run_classifier(x)
-#' plot_heatmap(x)
-plot_heatmap = function(x, model = 'binomial')
-{
-  stopifnot(inherits(x, "TAPACLOTH"))
-  
-  model = model %>% tolower()
-  
-  # Tibble 2 matrix
-  t2m = function(x){
-    m =  x[, 2:ncol(x)] %>% as.matrix()
-    colnames(m) = names(x)[2:length(names(x))]
-    rownames(m) = x$label
-    m
-  }
-  
-  # cli::cli_alert("Plotting model pheatmap")
-  
-  input_classes = x %>%
-    TAPACLOTH:::get_classifier(model = model) %>%
-    TAPACLOTH:::get_data() %>%
-    dplyr::mutate(
-      label = paste0(gene, " (", from, ") ", ref, '>', alt),
-      label_k = paste(ploidy, ' (', multiplicity, ')', sep = '')
-    )
-  
-  # Matrix of the classifications
-  input_classes_matrix = input_classes %>%
-    dplyr::mutate(outcome = ifelse(outcome, 1, 0)) %>%
-    dplyr::select(label, label_k, outcome) %>%
-    tidyr::pivot_wider(names_from = label_k, values_from = outcome)
-  
-  # Removed
-  # input_classes_matrix$other = 0
-  # no_classes = apply(input_classes_matrix[2:ncol(input_classes_matrix)], 1, function(x) all(x == 0))
-  # input_classes_matrix$other[no_classes] = 1
-  
-  # Idiotic formats
-  matrix_outcomes = input_classes_matrix %>% t2m()
-  
-  # p-values
-  pvalue_matrix = input_classes %>%
-    dplyr::select(label, label_k, pvalue) %>%
-    tidyr::pivot_wider(names_from = label_k, values_from = pvalue)
-  
-  p_matrix =  pvalue_matrix %>% t2m
-  
-  # Nicola - I don't understand why I have to use <, shouldn't it be >= to remove non-significant ones?
-  alpha_test = TAPACLOTH::get_params(x) %>% 
-    dplyr::filter(model == !!model) %>% 
-    pull(alpha)
-  
-  p_matrix[p_matrix > 1-alpha_test] = NA
-  
-  p_matrix = apply(p_matrix, c(1, 2), function(x) {
-    if (is.na(x)) return('')
-    if (x < alpha_test*0.001) return("***")
-    if (x < alpha_test*0.01) return("**")
-    return("*")
-  })
-  
-  # Read counts data
-  df_counts = input_classes %>%
-    dplyr::select(label, NV, DP, VAF) %>%
-    dplyr::distinct() %>%
-    data.frame()
-  
-  rownames(df_counts) = df_counts$label
-  df_counts = df_counts[, 2:ncol(df_counts)]
-  
-  # Roles
-  roles_all = input_classes$gene_role %>% unique()
-  roles_all = strsplit(roles_all, ',') %>% unlist %>% unique
-  roles_all_others = roles_all[!(roles_all %in% c("TSG", "oncogene", NA))]
-  
-  df_roles = input_classes %>%
-    dplyr::select(label, gene_role) %>%
-    dplyr::rename(role = gene_role) %>%
-    dplyr::distinct() %>%
-    rowwise() %>%
-    mutate(
-      TSG = grepl('TSG', role),
-      oncogene = grepl('oncogene', role),
-      other = sapply(roles_all_others, function(x)
-        grepl(x, role)) %>% any,
-      unknown = is.na(role)
-    ) %>%
-    dplyr::select(-role) %>%
-    as.data.frame()
-  
-  rownames(df_roles) = df_roles$label
-  df_roles = df_roles[,-1]
-  
-  # df_roles = apply(df_roles, 2, function(x) ifelse(x, 1, 0)) %>% data.frame
-  df_roles = apply(df_roles, 2, function(x)
-    ifelse(x, "YES", "NO")) %>% data.frame
-  
-  # Annotation rows
-  annotation_rows = cbind(df_counts, df_roles)
-  
-  # I decided we do not show these
-  annotation_rows = annotation_rows[,!apply(annotation_rows, 2, function(x)
-    all(x == "NO"))]
-  annotation_rows = annotation_rows[, colnames(annotation_rows) != 'NV']
-  annotation_rows = annotation_rows[, colnames(annotation_rows) != 'other']
-  
-  presence_annotation = 'darkgray'
-  onco_color = 'orange'
-  tsg_color = 'steelblue'
-  
-  annotation_colors = list(
-    TSG = c(`NO` = "white", `YES` = tsg_color),
-    oncogene = c(`NO` = "white", `YES` = onco_color),
-    other = c(`NO` = "white", `YES` = presence_annotation),
-    unknown = c(`NO` = "white", `YES` = presence_annotation),
-    # DP = RColorBrewer::brewer.pal(10, 'Purples'),
-    DP = viridis::viridis(10, direction = -1),
-    NV = RColorBrewer::brewer.pal(8, 'Purples'),
-    # VAF = RColorBrewer::brewer.pal(10, 'Spectral')
-    VAF = viridis::viridis(10, direction = -1)
-  )
-  
-  pheatmap::pheatmap(
-    mat = matrix_outcomes,
-    main = x$sample,
-    cluster_cols = FALSE,
-    fontsize_row = 6,
-    fontsize = 7,
-    cellwidth = 20,
-    cellheight = 10,
-    display_numbers = p_matrix,
-    number_color = 'white',
-    # border_color = NA
-    gaps_col = c(1, 2, 4, 6, 8),
-    breaks = c(-1, 0, 1),
-    color = c(`0` = ggplot2::alpha('gainsboro', .5), `1` = 'indianred3'),
-    legend_breaks = c(0, 1),
-    legend_labels = c(`0` = "Reject H0", `1` = "Fail to\nReject H0"),
-    annotation_row = annotation_rows,
-    annotation_colors = annotation_colors
-  )
-  
-}
diff --git a/R/plot_test.R b/R/plot_test.R
deleted file mode 100644
index e030fcd..0000000
--- a/R/plot_test.R
+++ /dev/null
@@ -1,169 +0,0 @@
-#' Visualize classification results for individual observations.
-#'
-#' @param x An object of class \code{'TAPACLOTH'} containing the classification results, as 
-#' produced by function `run_classifier`.
-#' @return An object of class \code{'ggplot2'}.
-#' @export
-#' @importFrom dplyr filter mutate rename select %>% 
-#' @examples
-#' x = init(mutations = example_data$data,
-#'          sample = example_data$sample,
-#'          purity = example_data$purity)
-#' model = "beta-binomial"
-#' x = run_classifier(
-#'     x = x, 
-#'     model = model, 
-#'     rho = 0.01,
-#'     karyotypes = c("1:0","1:1","2:0","2:1","2:2")
-#'     )
-#' plot_test(x = x,id = x$classifier[[model]]data$id[1],model = model)
-plot_test = function(x, assembly = F){
-  
-  stopifnot(inherits(x,"TAPACLOTH"))
-  
-  colors = CNAqc:::get_karyotypes_colors(c('1:0', '1:1', '2:0', '2:1', '2:2'))
-  colors = colors[c("1:0","1:1","2:1","2:2")]
-  names(colors) = sapply(names(colors), function(n){
-    strsplit(n,split = ":")[[1]] %>% as.integer() %>% sum()
-  })
-  
-  # names_colors = expand.grid(names(colors), 1:2) %>% apply(1, paste, collapse = ' ')
-  # colors = sapply(names_colors, function(n)
-  #   colors[strsplit(n, ' ')[[1]][1]])
-  # names(colors) = sapply(names_colors, function(n){
-  #   splitted = strsplit(n, ' ')[[1]]
-  #   k = splitted[1]
-  #   m = splitted[2]
-  #   paste0(strsplit(k, ':')[[1]] %>% as.integer() %>% sum(),"N (Mutated: ", m,"N)")
-  # })
-  
-  colors = c(colors, "out of sample" = 'gray')
-  
-  cutoff = x %>% get_params() %>% pull(cutoff)
-  
-  plots = lapply(x$classifier$data$id, function(id){
-    
-    # uncertainty = round(x %>%  get_classifier() %>% get_data() %>% 
-    #                       filter(id == !!id) %>% pull(uncertainty),2)
-    
-    
-    mdata = x %>% get_classifier(model) %>%
-      get_data() %>%
-      filter(id == !!id)
-    
-    # dataset = pull(mdata, density)[[1]] %>%
-    #   group_by(NV) %>%
-    #   summarise(
-    #     density,
-    #     Major,
-    #     minor,
-    #     multiplicity,
-    #     karyotype,
-    #     label,
-    #     peak,
-    #     cutoff,
-    #     uncertainty = 1 - max(density / sum(density))
-    #   ) %>%
-    #   ungroup()
-    
-    dataset = pull(mdata, density)[[1]]
-    
-    dataset = dataset %>% 
-      group_by(NV) %>% 
-      reframe(entropy = 1-max(density)/sum(density), density, ploidy, multiplicity, peak, cutoff, label, p_assign)
-    
-    dataset = lapply(dataset$label %>% unique(), function(l){
-      d = dataset %>% 
-        filter(label==l) 
-      n_points = 250
-      stride = max(round(nrow(d)/n_points),1)
-      d[seq(1,nrow(d),stride),]
-    }) %>% 
-      do.call(rbind, .)
-  
-    label = mdata$label
-    
-    scaleFactor = max(dataset$density)/max(dataset$entropy)
-    scaleFactor = ifelse(is.infinite(scaleFactor), 1, scaleFactor)
-    
-    dataset$multiplicity = factor(dataset$multiplicity)
-    dataset %>% 
-      mutate(ploidy = ifelse(label=="out of sample", label, ploidy))
-    dataset$ploidy = factor(dataset$ploidy)
-    
-    dataset %>%
-      ggplot() +
-      geom_line(aes(x = NV, y = density), color = 'white',  size = .5, alpha = 0)+
-      geom_line(
-        aes(x = NV, y = entropy * scaleFactor),
-        color = "deeppink4",
-        size = 0.5,
-        linetype = "longdash",
-        alpha = .4
-      ) +
-      CNAqc:::my_ggplot_theme() +
-      theme(axis.title.y.right = element_text(color="deeppink4"),
-            axis.text.y.right = element_text(color="deeppink4"))+
-      geom_point(data = dataset %>% maximise(),
-                 aes(x = NV,
-                     y = density,
-                     color = ploidy,
-                     shape = multiplicity
-                     ),
-                 size = 1) +
-      scale_color_manual(values = colors, breaks = dataset$ploidy %>% unique(), name = "Ploidy")+
-      scale_shape_manual(values = data_frame("1"=16,"2"=17), name = "Multiplicity")+
-      geom_line(data = dataset %>% maximise(),
-                aes(x = NV,
-                    y = density,
-                    color = ploidy,
-                    size = multiplicity))+
-      scale_size_manual(values = c("1"=.3,"2"=.3))+
-      scale_y_continuous("Likelihood", 
-                         sec.axis = sec_axis(~./scaleFactor, name = "Entropy"), 
-                         limits = c(0,max(dataset$density)))+
-      guides(size = "none")+
-      labs(
-        title = paste0(
-          mdata$from,
-          "; ",
-          mdata$ref,
-          ">",
-          mdata$alt,
-          "; ",
-          mdata$gene,
-          " (",
-          mdata$gene_role,
-          ")"
-        ),
-        subtitle = paste0(
-          "Classification: ",
-          label,
-          "\nSample: ",
-          get_sample(x),
-          "; Purity: ",
-          get_purity(x)
-        ),
-        caption = bquote(~alpha*" = "*.(cutoff)~
-                           "; Entropy: "*.(round(mdata$entropy,2))~
-                           " (mean: "*.(round(mdata$mean_entropy,2))*
-                         ")")
-        ) +
-      # guides(color = 'none') +
-      # geom_hline(data = dataset %>% group_by(label) %>% summarise(cutoff) %>% unique() %>% filter(label != "out of sample"),
-      #     mapping = aes(yintercept = cutoff,
-      #     color = label),
-      #     linetype = 'dashed',
-      #     size = .5
-      #   )+
-      geom_vline(
-        xintercept = get_NV(x, id),
-        color = 'black',
-        linetype = 'dashed',
-        size = .5
-      )
-  })
-  if(assembly){
-    ggpubr::ggarrange(plotlist = plots, ncol = 4)
-  } else plots
-}
\ No newline at end of file
diff --git a/R/plot_test_power.R b/R/plot_test_power.R
deleted file mode 100644
index b0745a1..0000000
--- a/R/plot_test_power.R
+++ /dev/null
@@ -1,242 +0,0 @@
-plot_test_power = function(null_model)
-
-{
-  inputs = null_model$density
-  coverage = null_model$coverage
-  p = null_model$purity/2
-  alpha_level = null_model$alpha_level
-  nvs = null_model$density$nv %>% as.vector()
-  l_a = null_model$nv[1]
-  r_a = null_model$nv[2]
-  l_v = null_model$vaf[1]
-  r_v = null_model$vaf[2]
-
-  model_string = "Binomial"
-  if(null_model$model == 'Beta-Binomial')
-    model_string = paste0("Beta-Binomial (rho = ", null_model$rho, ')')
-
-  col_loh = 'steelblue'
-  col_subclonal = 'indianred3'
-  col_clonal = 'forestgreen'
-
-  ggplot2::ggplot() +
-    CNAqc:::my_ggplot_theme() +
-    ggplot2::geom_rect(
-      data = data.frame(
-        xmin = 0,
-        xmax = nvs[l_a],
-        ymin = 0,
-        ymax = 1
-      ),
-      aes(
-        xmin = xmin,
-        xmax = xmax,
-        ymin = ymin,
-        ymax = ymax
-      ),
-      fill = col_subclonal,
-      alpha = .2
-    ) +
-    ggplot2::geom_rect(
-      data = data.frame(
-        xmax = coverage,
-        xmin = nvs[r_a],
-        ymin = 0,
-        ymax = 1
-      ),
-      aes(
-        xmin = xmin,
-        xmax = xmax,
-        ymin = ymin,
-        ymax = ymax
-      ),
-      fill = col_loh,
-      alpha = .2
-    ) +
-    ggplot2::geom_rect(
-      data = data.frame(
-        xmax = nvs[l_a],
-        xmin = nvs[r_a],
-        ymin = 0,
-        ymax = 1
-      ),
-      aes(
-        xmin = xmin,
-        xmax = xmax,
-        ymin = ymin,
-        ymax = ymax
-      ),
-      fill = col_clonal,
-      alpha = .2
-    ) +
-    ggplot2::geom_point(
-      data = inputs %>% filter(nv < nvs[l_a]),
-      aes(x = nv, y = p),
-      size = .6,
-      color = col_subclonal
-    ) +
-    ggplot2::geom_point(
-      data = inputs %>% filter(nv > nvs[r_a]),
-      aes(x = nv, y = p),
-      size = .6,
-      color = col_loh
-    ) +
-    ggplot2::geom_point(
-      data = inputs %>% filter(nv >= nvs[l_a], nv <= nvs[r_a]),
-      aes(x = nv, y = p),
-      size = 1,
-      color = col_clonal
-    ) +
-    ggplot2::geom_point(
-      data = inputs,
-      aes(x = nv, y = VAF),
-      size = .6,
-      shape = 3,
-      color = 'gray'
-    ) +
-    ggplot2::geom_point(
-      data = inputs %>% filter(nv == nvs[l_a]),
-      aes(x = nv, y = VAF),
-      size = 3,
-      color = col_subclonal
-    ) +
-    ggplot2::geom_segment(
-      data = inputs %>% filter(nv == nvs[l_a]),
-      aes(
-        x = nvs[l_a],
-        y = VAF,
-        xend = coverage,
-        yend = VAF
-      ),
-      linetype = 'dashed',
-      color = col_subclonal
-    ) +
-    ggplot2::geom_segment(
-      data = inputs %>% filter(nv == nvs[l_a]),
-      aes(
-        x = nvs[l_a],
-        y = VAF,
-        xend = nvs[l_a],
-        yend = 0
-      ),
-      linetype = 'dashed',
-      color = col_subclonal
-    ) +
-    ggplot2::geom_point(
-      data = inputs %>% filter(nv == nvs[r_a]),
-      aes(x = nv, y = VAF),
-      size = 3,
-      color = col_loh
-    ) +
-    ggplot2::geom_segment(
-      data = inputs %>% filter(nv == nvs[r_a]),
-      aes(
-        x = nvs[r_a],
-        y = VAF,
-        xend = coverage,
-        yend = VAF
-      ),
-      linetype = 'dashed',
-      color = col_loh
-    ) +
-    ggplot2::geom_segment(
-      data = inputs %>% filter(nv == nvs[r_a]),
-      aes(
-        x = nvs[r_a],
-        y = VAF,
-        xend = nvs[r_a],
-        yend = 1
-      ),
-      linetype = 'dashed',
-      color = col_loh
-    ) +
-    ggplot2::geom_text(
-      x = nvs[l_a] - 5,
-      y = 1,
-      label = 'subclonal',
-      hjust = 1,
-      size = 3,
-      color = col_subclonal
-    ) +
-    ggplot2::geom_text(
-      x = nvs[r_a] + 5,
-      y = 0,
-      label = 'clonal LOH',
-      hjust = 0,
-      size = 3,
-      color = col_loh
-    ) +
-    ggplot2::labs(
-      x = 'NV',
-      y = "1 - P(X > NV)",
-      caption = model_string,
-      title = paste0("Coverage ", coverage, ' with purity ', p*2),
-      subtitle = paste0('Alpha-level: ', alpha_level)
-    ) +
-    ggplot2::coord_cartesian(clip = 'off') +
-    ggplot2::scale_y_continuous(sec.axis = sec_axis(~ ., name = 'VAF | coverage')) +
-    ggplot2::theme(axis.line.y.right = element_line(color = "gray")) +
-    ggplot2::annotation_custom(
-      grid::textGrob(paste('>', round(r_v, 2)), gp = grid::gpar(col = col_loh, fontsize = 8)),
-      xmin = coverage,
-      xmax = coverage,
-      ymin = r_v + .03,
-      ymax = r_v + .03
-    ) +
-    ggplot2::annotation_custom(
-      grid::textGrob(
-        paste('<', round(l_v, 2)),
-        gp = grid::gpar(col = col_subclonal, fontsize = 8)
-      ),
-      xmin = coverage,
-      xmax = coverage,
-      ymin = l_v - .03,
-      ymax = l_v - .03
-    ) +
-    ggplot2::annotate(
-      "text",
-      x = 0,
-      y = .95,
-      label = "Subclonal",
-      hjust = 0,
-      size = 3,
-      color = col_subclonal
-    ) +
-    ggplot2::annotate(
-      "text",
-      x = coverage,
-      y = .95,
-      label = "Clonal LOH",
-      hjust = 1,
-      size = 3,
-      color = col_loh
-    ) +
-    ggplot2::annotate(
-      "text",
-      x = coverage * p,
-      y = .95,
-      label = "Clonal",
-      hjust = .5,
-      size = 3,
-      color = col_clonal
-    )
-}
-
-example_cartoons = function()
-{
-  ggpubr::ggarrange(
-    plot_test_power(140, .3),
-    plot_test_power(140, .3, model = 'betabinomial', rho = 0.001),
-    plot_test_power(140, .3, model = 'betabinomial', rho = 0.01),
-    ncol = 1,
-    nrow = 3
-  )
-
-  ggpubr::ggarrange(
-    plot_test_power(700, .4),
-    plot_test_power(700, .4, model = 'betabinomial', rho = 0.001),
-    plot_test_power(700, .4, model = 'betabinomial', rho = 0.01),
-    ncol = 1,
-    nrow = 3
-  )
-}
diff --git a/R/print.INCOMMON.R b/R/print.INCOMMON.R
new file mode 100644
index 0000000..396cd0b
--- /dev/null
+++ b/R/print.INCOMMON.R
@@ -0,0 +1,78 @@
+#' Plot for class \code{'INCOMMON'}.
+#'
+
+#' @description
+#'
+#' If the terzile model is used, the default plot is a histogram of the VAF spectrum is plotted,
+#' with expected clonal peak, purity and VAF of mutations affecting the target gene
+#' highlighted. If the Binomial or Beta-Binomial model is used, it includes
+#' a plot showing details of the used statistical test in the bottom panel.
+#'
+#' @param x An obj of class \code{'INCOMMON'}.
+#' @param... Default S3 method parameter.
+#'
+#' @return Nothing.
+#'
+#' @export
+#'
+#' @examples
+#' input = init(mutations = example_data$data[1,], sample = example_data$sample, purity = example_data$purity)
+#' x = run_classifier(input, alpha_level = 1e-3, model = "Binomial")
+#' x = plot_test(x)
+#' plot.INCOMMON(x)
+
+plot.INCOMMON = function(x, ...) {
+  stopifnot(inherits(x, "INCOMMON"))
+  lapply(names(x$classifier), function(model){
+    lapply(x$classifier[[model]]$data$id, function(id){
+      plot_test(x, id = id, model = model)
+    })
+  })
+}
+#' Print for class \code{'INCOMMON'}.
+#' @param x An obj of class \code{'INCOMMON'}.
+#' @param ... Default S3 method parameter.
+#'
+#' @return Nothing.
+#' @import cli
+#' @import crayon
+#' @importFrom dplyr filter mutate rename select %>% 
+#' @export
+#'
+#' @examples
+#' x = init(mutations = example_data$data,
+#'          sample = example_data$sample,
+#'          purity = example_data$purity,
+#'          tumor_type = example_data$tumor_type)
+#' x = classify(
+#'     x = x, 
+#'     priors = priors,
+#'     entropy_cutoff = 0.2,
+#'     rho = 0.01,
+#'     karyotypes = c("1:0","1:1","2:0","2:1","2:2")
+#'     )
+#' print(x)
+print.INCOMMON = function(x, ...) {
+  stopifnot(inherits(x, "INCOMMON"))
+  ## Print input data
+  cli::cli_rule(
+    paste(
+      crayon::bgMagenta(crayon::black("[ INCOMMON ] ")),
+      'Sample {.field {x$sample}} ({.field {x$tumor_type}}), with purity {.field {x$purity}}'
+    )
+  )
+  
+  if ("fit" %in% names(x)) {
+
+      cli::cli_rule(
+        paste(
+          crayon::bgMagenta(crayon::black("[ INCOMMON ] ")),
+          'Classified mutations using Beta-binomial model',
+                 'with overdispersion parameter {.field {parameters(x)$rho}} and entropy cutoff {.field {parameters(x)$entropy_cutoff}}',
+          ''
+        ))
+      print(classification(x))
+  } else{
+    data(x)
+  }
+}
diff --git a/R/print.tapacloth.R b/R/print.tapacloth.R
deleted file mode 100644
index be0c756..0000000
--- a/R/print.tapacloth.R
+++ /dev/null
@@ -1,100 +0,0 @@
-#' Plot for class \code{'TAPACLOTH'}.
-#'
-
-#' @description
-#'
-#' If the terzile model is used, the default plot is a histogram of the VAF spectrum is plotted,
-#' with expected clonal peak, purity and VAF of mutations affecting the target gene
-#' highlighted. If the Binomial or Beta-Binomial model is used, it includes
-#' a plot showing details of the used statistical test in the bottom panel.
-#'
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param... Default S3 method parameter.
-#'
-#' @return Nothing.
-#'
-#' @export
-#'
-#' @examples
-#' input = init(mutations = example_data$data[1,], sample = example_data$sample, purity = example_data$purity)
-#' x = run_classifier(input, alpha_level = 1e-3, model = "Binomial")
-#' x = plot_test(x)
-#' plot.TAPACLOTH(x)
-
-plot.TAPACLOTH = function(x, ...) {
-  stopifnot(inherits(x, "TAPACLOTH"))
-  lapply(names(x$classifier), function(model){
-    lapply(x$classifier[[model]]$data$id, function(id){
-      plot_test(x, id = id, model = model)
-    })
-  })
-}
-#' Print for class \code{'TAPACLOTH'}.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param ... Default S3 method parameter.
-#'
-#' @return Nothing.
-#' @import cli
-#' @import crayon
-#' @importFrom dplyr filter mutate rename select %>% 
-#' @export
-#'
-#' @examples
-#' x = init(mutations = example_data$data,
-#'          sample = example_data$sample,
-#'          purity = example_data$purity)
-#' x = run_classifier(
-#'     x, 
-#'     alpha_level = 1e-3, 
-#'    model = "Binomial")
-#' x = estimate_purity(x = x, model = "binomial", eps = 0.01)
-#' print(x)
-print.TAPACLOTH = function(x, ...) {
-  stopifnot(inherits(x, "TAPACLOTH"))
-  ## Print input data
-  cli::cli_rule(
-    paste(
-      crayon::bgMagenta(crayon::black("[ TAPACLOTH ] ")),
-      'Input data for sample {.field {x$sample}}, with purity {.field {x$purity}}'
-    )
-  )
-  
-  print(x$data)
-
-  if ("purity_estimate" %in% names(x)){
-      cli::cli_rule(
-        paste(
-          crayon::bgMagenta(crayon::black("[ TAPACLOTH ] ")),
-          'Purity estimate using ',
-          crayon::bgYellow(crayon::black("[ BMix ] ")),
-          'with Beta-binomial model'
-        )
-      )
-      print(tibble(
-        purity = get_purity(x),
-        reliability = get_reliability(x),
-        purity_bmix = get_purity_bmix(x),
-      ))
-    
-    cat("\n")
-  }
-  
-  if ("classifier" %in% names(x)) {
-
-      cli::cli_rule(
-        paste(
-          crayon::bgMagenta(crayon::black("[ TAPACLOTH ] ")),
-          'Test using Beta-binomial model',
-                 'with overdispersion parameter {.field {x$classifier$params$rho}} and likelihood cutoff {.field {x$classifier$params$cutoff}}',
-          ''
-        ))
-      print(get_classifier(x) %>% 
-              get_data() %>% 
-              dplyr::select(id, NV, DP, VAF, 
-                            gene, gene_role,
-                            state, label,
-                            ploidy, multiplicity,
-                            entropy)
-            )
-  }
-}
diff --git a/R/purity_from_fit.R b/R/purity_from_fit.R
deleted file mode 100644
index 2a7be84..0000000
--- a/R/purity_from_fit.R
+++ /dev/null
@@ -1,20 +0,0 @@
-purity_from_fit = function(n_binomials, peaks, purity, eps) {
-  out = NA
-  if (n_binomials == 3)
-    out = peaks[2] * 2
-  if (n_binomials == 1)
-    out = peaks[1] * 2
-  if (n_binomials == 2) {
-    purity_hyp = c(min(peaks[1] * 2, 1), min(peaks[2] * 2, 1)) # in this case we have two equivalent putative purities
-    if (!is.na(purity) &
-        min(abs(purity_hyp - purity)) <= eps)
-      # check if at least one is close to the input one
-      out = purity_hyp[which.min(abs(purity_hyp - purity))] # choose the estimate that is closest to input
-    if (is.na(out)) {
-      cli::cli_alert(
-        "Purity could not be estimated reliably. Check results of the fit in the output figure"
-      )
-    }
-  }
-  return(out)
-}
\ No newline at end of file
diff --git a/R/run_classifier.R b/R/run_classifier.R
deleted file mode 100644
index a40cd06..0000000
--- a/R/run_classifier.R
+++ /dev/null
@@ -1,103 +0,0 @@
-#' Classify mutations using a (Beta-)Binomial model-based test.
-#'
-#' @param x An object of class \code{'TAPACLOTH'} generated with function `init`.
-#' @param cutoff Likelihood cut-off for class assignment.
-#' @param model Model used for the classification task, either "Binomial" (no over-dispersion) 
-#' or "Beta-Binomial" (over-dispersion included), that will be used as the expected 
-#' distribution for the number of reads with variant at fixed coverage and purity.
-#' @param rho If "Beta-Binomial" model is selected, this parameter tunes the over-dispersion
-#' of the expected distribution used for the test.
-#' @param karyotypes Karyotypes to be included among the possible classes.
-#' @return An object of class `TAPACLOTH` containing the input plus
-#' the classification data and paramters.
-#' @export
-#' @importFrom dplyr filter mutate rename select %>% 
-#' @examples
-#' x = init(mutations = example_data$data,
-#'          sample = example_data$sample,
-#'          purity = example_data$purity)
-#' x = run_classifier(
-#'     x = x, 
-#'     model = "Beta-Binomial", 
-#'     rho = 0.01,
-#'     karyotypes = c("1:0","1:1","2:0","2:1","2:2")
-#'     )
-#' print(x)
-run_classifier = function(x,
-                          cutoff = 0.75,
-                          rho = 0.01,
-                          karyotypes = c("1:0","1:1","2:0","2:1","2:2"),
-                          priors = NULL,
-                          gene_role_specific = FALSE,
-                          assign_extremes = FALSE
-                          )
-  {
-  stopifnot(inherits(x, "TAPACLOTH"))
-  
-  # Output
-  test = x
-  if (!("classifier" %in% names(test)))
-    test$classifier = list()
-  
-  cli::cli_h1(
-      "TAPACLOTH clonality/Zygosity testing for sample {.field {x$sample}}"
-    )
-    cat("\n")
-    
-  check_input(x)
-    
-  cli::cli_alert_info("Computing likelihoods and uncertainties.")
-    
-  x = idify(x)
-    
-  tests = lapply(x$data$id, function(id) {
-    if(x$data %>% 
-      dplyr::filter(id==!!id) %>% 
-      nrow() > 1){
-      cli_alert_warning(text = "More than one mutation mapped at: {.field {id}}")
-      x$data %>% 
-        dplyr::filter(id==!!id) 
-      cli_alert_warning(text = "Keeping first one (consider going back to input data)")
-      w = which(x$data$id==id)
-      x$data = x$data[-w[2:length(w)],]
-        
-    }
-    # If classifying with a bias towards gene role, adapt karyotypes list accordingly.
-    k_reduced = karyotypes
-    if(gene_role_specific & !(x %>% get_gene_role(id)  %>% is.na)){
-      if(x %>% get_gene_role(id) == "TSG") k_reduced = c("1:0","1:1","2:0")
-      if(x %>% get_gene_role(id) == "oncogene") k_reduced = c("1:1","2:1","2:2")
-    } 
-    
-    # Compute likelihoods
-    binomial_test(
-      test = get_NV(x, id),
-      DP = get_DP(x, id),
-      gene = get_gene(x, id),
-      priors = priors,
-      purity = get_purity(x),
-      cutoff = cutoff,
-      rho = rho,
-      karyotypes = k_reduced,
-      assign_extremes
-    )
-  }) %>% 
-    do.call(rbind, .)
-  
-  
-    test$classifier = list(
-      params = tibble(cutoff = cutoff,
-                      rho = rho),
-      data = bind_cols(x %>% get_data(), tests)
-    )
-    
-    test$classifier$data = test %>% 
-      get_classifier() %>% 
-      get_data() %>% 
-      reduce_classes() %>% 
-      add_per_state_probabilities()
-    
-  return(test)
-}
-
-
diff --git a/R/run_test.R b/R/run_test.R
deleted file mode 100644
index 64156bf..0000000
--- a/R/run_test.R
+++ /dev/null
@@ -1,5 +0,0 @@
-run_test = function(nv, null_model){
-  if(nv > null_model$nv[2]) return("Clonal LOH")
-  if(nv > null_model$nv[1]) return("Clonal")
-  return("Subclonal")
-  }
diff --git a/R/test_setup.R b/R/test_setup.R
deleted file mode 100644
index ddc5292..0000000
--- a/R/test_setup.R
+++ /dev/null
@@ -1,122 +0,0 @@
-#' Compute parameters and distribution for null hypothesis.
-#'
-#' @param coverage The sequencing coverage at the locus of mutation.
-#' @param purity Sample purity.
-#' @param rho The overdisperion parameter for "Beta-Binomial" model.
-#' @param alpha_level The confidence level of the test.
-#' @param model Model used for the test, either "Binomial" or "Beta-Binomial".
-#' @return A list.
-#' @export
-#' @importFrom dplyr filter mutate rename select %>% 
-#' @import VGAM 
-#' @import stringr
-#' @examples
-#' null_model = test_setup(coverage = 500, purity = 1.0, rho = 0.01, alpha_level = 0.01, model = 'binomial') 
-#' print(null_model)
-test_setup = function(coverage = 500,
-                      purity = 1.0,
-                      rho = 0.01,
-                      threshold = 0.1,
-                      model = 'binomial',
-                      karyotypes = c("1:0", "1:1", "2:0", "2:1", "2:2")
-)
-{
-
-  # Range of NV values
-  nvs = 1:coverage
-
-  # Compute Binomial or Beta-Binomial probability for NV values in range
-  log_p = NULL
-  # p = purity/2
-  # if ((model %>% tolower()) == 'binomial')
-  # {
-  #   log_p = sapply(nvs, dbinom, size = coverage, prob = p)
-  # }
-  # else
-  # {
-  #   log_p = sapply(
-  #     nvs,
-  #     VGAM::dbetabinom,
-  #     size = coverage,
-  #     prob = p,
-  #     rho = rho
-  #   )
-  # }
-  
-  log_p = lapply(karyotypes, function(karyotype) {
-    alleles = stringr::str_split(string = karyotype, pattern = ":") %>% unlist() %>% as.integer()
-    ploidy = sum(alleles)
-    lapply(1:max(alleles), function(mult) {
-      if ((model %>% tolower()) == 'binomial') {
-        log_p = sapply(nvs,
-                       dbinom,
-                       size = coverage,
-                       prob = mult * purity / (2 * (1 - purity) + purity * ploidy))
-      }
-      else {
-        log_p = sapply(
-          nvs,
-          VGAM::dbetabinom,
-          size = coverage,
-          prob = mult * purity / (2 * (1 - purity) + purity * ploidy),
-          rho = rho
-        )
-      }
-      
-      # Compute P(X > NV) for each NV value
-      # p_x = cumsum(log_p)
-      # Find l_a such that P(X <= l_a) < alpha
-      # l_a = which(p_x < alpha_level, arr.ind = TRUE) %>% max
-      # 
-      # # Find r_a such that P(X > r_a) < 1 - alpha
-      # r_a = which(p_x > 1 - alpha_level, arr.ind = TRUE) %>% min
-
-      # Compute two-tailed p-value for each NV value
-      p_x = sapply(nvs, function(nv){log_p[which(log_p <= log_p[nv])] %>% sum()})
-      # p_x = 1-p_x
-      # p_x = log_p
-      
-      # Find left extremum NV l_a such that p-value < alpha
-      l_a = which(p_x > threshold, arr.ind = TRUE) %>% min
-      
-      # Find right extremum NV l_a such that p-value < alpha
-      r_a = which(p_x > threshold, arr.ind = TRUE) %>% max
-      
-      # Adjustments for plots when test fails
-      if (is.infinite(l_a))
-        l_a = 1
-      if (is.infinite(r_a))
-        r_a = coverage
-      
-      # Translate NV cutoffs in VAF space
-      
-      vafs = nvs / coverage
-      l_v = vafs[l_a]
-      r_v = vafs[r_a]
-      
-      return(tibble(
-        karyotype = karyotype,
-        multiplicity = mult,
-        inputs = list(tibble(nv = nvs,
-                             p = p_x,
-                             VAF = vafs)),
-          l_a = l_a,
-          r_a = r_a,
-          l_v = l_v,
-          r_v = r_v
-      ))
-    }) %>% do.call(rbind, .)
-  }) %>% do.call(rbind, .)
-  
-  
-  # cli::cli_alert_info("Computing p-values.")
-
-  return(list(
-    model = model,
-    rho = rho,
-    coverage = coverage,
-    purity = purity,
-    threshold = threshold,
-    test = log_p
-  ))
-}
diff --git a/R/utils.R b/R/utils.R
index 38e1fb2..5314923 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,157 +1,112 @@
-get_data = function(x){
+data = function(x){
   return(x$data)
 }
 
-get_sample = function(x){
+samples = function(x){
   return(x$sample)
 }
 
-get_purity = function(x){
+purity = function(x){
   return(unique(x$purity))
 }
 
-#' Getter for class \code{'TAPACLOTH'}.
+tumor_type = function(x){
+  return(unique(x$tumor_type))
+}
+
+
+#' Getter for class \code{'INCOMMON'}.
 #' @description
-#' Get significant classification data for the specified model, if already tested.
-#' @param x An obj of class \code{'TAPACLOTH'}.
+#' Get classification data for specific selected model.
+#' @param x An obj of class \code{'INCOMMON'}.
 #' @param model Model used in the test from which to get classification data.
-#' @return A tibble.
+#' @return A tibble with classification data.
 #' @export
-get_classes = function(x, model){
-  stopifnot(inherits(x, "TAPACLOTH"))
-  y = x$classifier[[model]]$data %>% 
-    dplyr::select(chr, from, to, ref, alt, karyotype, multiplicity, outcome)
-  return(y)
+classification = function(x) {
+  stopifnot(inherits(x, "INCOMMON"))
+  stopifnot("fit" %in% names(x))
+  stopifnot("classification" %in% names(x$fit))
+  x$fit$classification
 }
 
-#' Getter for class \code{'TAPACLOTH'}.
+#' Getter for class \code{'INCOMMON'}.
 #' @description
 #' Get model parameters of the performed classification tests.
-#' @param x An obj of class \code{'TAPACLOTH'}.
+#' @param x An obj of class \code{'INCOMMON'}.
 #' @return A tibble containing parameters for all the models used in the classification.
 #' @export
 #' 
-get_params = function(x) {
-  stopifnot(inherits(x, "TAPACLOTH"))
-  x$classifier$params
+parameters = function(x) {
+  stopifnot(inherits(x, "INCOMMON"))
+  stopifnot("fit" %in% names(x))
+  stopifnot("params" %in% names(x$fit))
+  x$fit$params
 }
 
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' Get classification data for a specific gene.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param gene_id The name of the gene.
-#' @return A tibble with gene-specific classification data.
-#' @export
-gene_label = function(x, gene_id){
-  stopifnot(inherits(x, "TAPACLOTH"))
-  x = idify(x)
-  y = x$classifier$data %>% 
-    dplyr::filter(gene == gene_id)
-  return(tibble(id = y$id,
-                label = y$label))
-}
 
-#' Getter for class \code{'TAPACLOTH'}.
+#' Getter for class \code{'INCOMMON'}.
 #' @description
-#' Get point and mean classification entropy data for a specific gene.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param gene_id The name of the gene.
-#' @return A tibble with gene-specific classification data.
+#' Get model parameters of the performed classification tests.
+#' @param x An obj of class \code{'INCOMMON'}.
+#' @return A tibble containing parameters for all the models used in the classification.
 #' @export
-gene_entropy = function(x, gene_id){
-  stopifnot(inherits(x, "TAPACLOTH"))
-  x = idify(x)
-  y = x$classifier$data %>% 
-    dplyr::filter(gene == gene_id)
-  return(tibble(id = y$id,
-                entropy = y$entropy,
-                mean_entropy = y$mean_entropy))
+#' 
+posterior = function(x, id) {
+  stopifnot(inherits(x, "INCOMMON"))
+  stopifnot("fit" %in% names(x))
+  stopifnot("posterior" %in% names(x$fit))
+  stopifnot(id %in% names(x$fit$posterior))
+  x$fit$posterior[[id]]
 }
 
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' Get classification data for specific selected model.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param model Model used in the test from which to get classification data.
-#' @return A tibble with classification data.
-#' @export
-get_classifier = function(x, model = NULL) {
-  stopifnot(inherits(x, "TAPACLOTH"))
-  stopifnot("classifier" %in% names(x))
-  x$classifier
-  }
-
 idify = function(x){
-  y = get_data(x)
-  y = y %>% 
+  x$data = data(x) %>% 
     mutate(id = paste(chr,from,to,ref,alt,sep = ":"))
-  x$data = y
   return(x)
 }
 
 unidify = function(x){
-  y = get_data(x)
-  y = y %>% 
+  x$data = data(x) %>% 
     dplyr::select(-id)
-  x$data = y
   return(x)
 }
 
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' Get coverage for a specific mutation in the sample.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param mutation_id Coordinates of mutation in the form of a string 
-#' containing `chr`,`from`,`to`,`alt`,`ref` coordinates, colon separated.
-#' @return DP of the mutation.
-#' @export
-get_DP = function(x, id){
+ids = function(x){
+  if(!("id" %in% colnames(data(x)))) x = idify(x)
+  data(x) %>% pull(id) %>% unique()
+}
+
+info = function(x, mutation_id){
+  if(!("id" %in% colnames(data(x)))) x = idify(x)
+  out = data(x) %>% dplyr::filter(id == mutation_id)
+  if("fit" %in% names(x)) out = classification(x) %>% dplyr::filter(id == mutation_id)
+  out
+}
+
+
+DP = function(x, id){
   x = idify(x)
-  x$data %>% 
+  data(x) %>% 
     dplyr::filter(id == !!id) %>% 
     pull(DP)
 }
 
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' Get number of reads with variant for a specific mutation in the sample.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param mutation_id Coordinates of mutation in the form of a string 
-#' containing `chr`,`from`,`to`,`alt`,`ref` coordinates, colon separated.
-#' @return NV of the mutation.
-#' @export
-get_NV = function(x, id){
+NV = function(x, id){
   x = idify(x)
-  x$data %>% 
+  data(x) %>% 
     dplyr::filter(id == !!id) %>% 
     pull(NV)
 }
 
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' Get variant allele frequency (VAF) for a specific mutation in the sample.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param mutation_id Coordinates of mutation in the form of a string 
-#' containing `chr`,`from`,`to`,`alt`,`ref` coordinates, colon separated.
-#' @return VAF of the mutation.
-#' @export
-get_VAF = function(x, mutation_id){
+
+VAF = function(x, mutation_id){
   x = idify(x)
-  x$data %>% 
+  data(x) %>% 
     dplyr::filter(id == mutation_id) %>% 
     pull(VAF)
 }
 
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' Get ID of the gene affected by the specified mutation.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param mutation_id Coordinates of mutation in the form of a string 
-#' containing `chr`,`from`,`to`,`alt`,`ref` coordinates, colon separated.
-#' @return A tibble with the name of the gene affected by the specified mutation.
-#' @export
-get_gene = function(x, mutation_id){
+gene = function(x, mutation_id){
   x = idify(x)
   x$data %>% 
     dplyr::filter(id == mutation_id) %>% 
@@ -165,47 +120,17 @@ get_gene_role = function(x, id){
     pull(gene_role)
 }
 
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' Get coordinates of mutation(s) mapped on a specified gene.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param gene_name Name of the gene affected by the mutation.
-#' @return A list of mutation coordinates.
-#' @export
-get_coord = function(x, gene_name){
-  x %>% 
-    idify() %>% 
-    get_data() %>% 
-    dplyr::filter(gene == gene_name) %>% 
-    pull(id) %>% 
-    strsplit(., split = ":")
-}
-
-get_mass = function(x, null_model, id){
-  y = null_model$test %>% 
-    dplyr::select(karyotype, multiplicity, l_a, r_a)
-  
-  y$id = id
-  
-  y$mass = sapply(null_model$test$inputs, function(s) {
-    s$p[get_NV(x, id)]
-  })
-  
-  y$gene = get_gene(x, id)
-  
-  return(y)
-}
 
-#' Plot function for class \code{'TAPACLOTH'}.
+#' Plot function for class \code{'INCOMMON'}.
 #' @description
 #' Plot results of the classification under the specified model and for the specified gene.
-#' @param x An obj of class \code{'TAPACLOTH'}.
+#' @param x An obj of class \code{'INCOMMON'}.
 #' @param gene_name Name of gene affected by the mutation.
 #' @param model Model used for classification.
 #' @return A tibble with classification data for the specified mutation.
 #' @export
 plot_gene = function(x,model,gene_name){
-  stopifnot(inherits(x, "TAPACLOTH"))
+  stopifnot(inherits(x, "INCOMMON"))
   model = model %>% tolower()
   ids = get_id(x,gene_name)
   lapply(ids, function(i){
@@ -213,130 +138,29 @@ plot_gene = function(x,model,gene_name){
   })
 }
 
-#' Plot function for class \code{'TAPACLOTH'}.
-#' @description
-#' Plot results of the BMix fit used for purity estimation, under the specified model.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param model Model used for purity estimate
-#' @return A plot of BMix fit.
-#' @export
-plot_bmix = function(x){
-  y = x$purity_estimate$plot_bmix
-  return(y)
-}
-
-
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' Extract data and parameters of purity estimation.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param model Model used for purity estimation
-#' @return Purity estimate data.
-#' @export
-get_purity_estimate = function(x){
-  stopifnot(inherits(x, "TAPACLOTH"))
-  y = x$purity_estimate
-  return(y)
-}
-
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' Extract the sample purity as estimated using the specified model
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param model Model used for purity estimation
-#' @return Sample purity as obtained by BMix purity estimation procedure.
-#' @export
-get_purity_bmix = function(x){
-  stopifnot(inherits(x, "TAPACLOTH"))
-  y = get_purity_estimate(x)
-  return(y$purity)
-}
-
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' Extract reliability of input sample purity as compared to TAPACLOTH estimate using the specified model.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param model Model used for purity estimation
-#' @return Reliability of input purity estimate.
-#' @export
-get_reliability = function(x){
-  stopifnot(inherits(x, "TAPACLOTH"))
-  y = get_purity_estimate(x)
-  return(y$reliability)
-}
-
-get_threshold = function(x, model){
-  y = get_classifier(x, model)
-  y$params$threshold
-}
-
-get_rho = function(x){
-  y = get_classifier(x, model = "beta-binomial")
-  y$params$rho
-}
-
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' List models used for classification tests.
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @return Model names.
-#' @export
-models_avail = function(x){
-  stopifnot(inherits(x, "TAPACLOTH"))
-  return(names(x$classifier))
-}
-
-get_ploidy = function(k){
-  stringr::str_split(k, pattern = ":")[[1]] %>% as.integer() %>% sum()}
-
-#' Getter for class \code{'TAPACLOTH'}.
-#' @description
-#' Get ID of the mutation(s) affecting the specified gene
-#' @param x An obj of class \code{'TAPACLOTH'}.
-#' @param gene_name Name of the selected gene.
-#' @return ID( of mutation(s).
-#' @export
-get_id = function(x, gene_name){
-  x = idify(x)
-  x$data %>% 
-    dplyr::filter(gene == gene_name) %>% 
-    pull(id)
-}
-
-closer_dist = function(null_model, nv, karyotypes) {
-  i = null_model$test %>% 
-    rowwise() %>%
-    mutate(dist = min(nv - l_a, nv - r_a)) %>% 
-    pull(dist) %>% 
-    abs() %>% 
-    which.min()
-  return(i)
-}
-
-# Maxima
-maximise = function(x)
-{
-  x %>%
-    group_by(NV) %>%
-    filter(density == max(density)) %>%
-    ungroup()
-}
-
 # Prior getter
 
-get_prior = function(x, gene, label){
+get_prior = function(x, gene, tumor_type){
   
   if(is.null(x)) {
     cli::cli_alert("No prior probabilities provided")
     return(1)
-  } else {
-    out = x %>% filter(gene == !!gene, label == !!label) %>% pull(p)
-  if(out %>% length() == 0){
-    cli::cli_alert("No prior probabilitiy specified for {.field {gene}}")
+  }
+  
+  if(!(gene %in% x$gene)) {
+    cli::cli_alert("No prior probability specified for {.field {gene}}")
     return(1)
   }
-  else if (out %>% length() > 0) return(out)
-    }
+  
+  if(tumor_type %in% (x %>% dplyr::filter(gene == !!gene) %>% dplyr::pull(tumor_type))) {
+    out = x %>% dplyr::filter(gene == !!gene, tumor_type == !!tumor_type)
+  } else {
+    cli::cli_alert("No {.field {tumor_type}}-specific prior probability specified for {.field {gene}}")
+    cli::cli_alert("Using a pan-cancer prior")
+    out = x %>% dplyr::filter(gene == !!gene, tumor_type == 'PANCA')
+    } 
+  
+  return(out)
 }
 
 
@@ -350,7 +174,7 @@ check_input = function(x){
     cli::cli_abort("Unrecogniseable gene names, will not proceed.")
   
   if(x$data$gene_role %>% class() != "character" | 
-     setdiff(x$data$gene_role,c("TSG", "oncogene")) %>% length() != 0) 
+     setdiff(x$data$gene_role, c("TSG", "oncogene", NA)) %>% length() != 0) 
     cli::cli_abort("Unrecogniseable gene roles, will not proceed.")
   
   if(x$data$chr %>% class() != "character") 
@@ -410,3 +234,17 @@ add_per_state_probabilities = function(x, NV){
            p_assign_all = list(probs))
   }) %>% do.call(rbind, .)
 } 
+
+remove_mutation = function(x, mutation_id){
+  x$data = x$data %>% dplyr::filter(id != mutation_id)
+  if('fit' %in% names(x)) x$fit = x$fit %>% dplyr::filter(id != mutation_id)
+}
+
+# Palettes
+
+ploidy_colors = CNAqc:::get_karyotypes_colors(c('1:0', '1:1', '2:0', '2:1', '2:2'))
+ploidy_colors = ploidy_colors[c("1:0","1:1","2:1","2:2")]
+names(ploidy_colors) = sapply(names(ploidy_colors), function(n){
+  strsplit(n,split = ":")[[1]] %>% as.integer() %>% sum()
+})
+ploidy_colors = c(ploidy_colors, "Tier-2" = 'gray')
diff --git a/README.md b/README.md
index 86d8d89..2f86e1f 100644
--- a/README.md
+++ b/README.md
@@ -5,7 +5,7 @@
 
 <!-- badges: start -->
 
-[![R-CMD-check](https://github.com/caravagnalab/TAPACLOTH/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/caravagnalab/TAPACLOTH/actions/workflows/R-CMD-check.yaml)
+[![R-CMD-check](https://github.com/caravagnalab/INCOMMON/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/caravagnalab/INCOMMON/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 INCOMMON is a tool for the INference of COpy number and 
@@ -20,7 +20,7 @@ or with high ploidy and low multiplicity).
 
 #### Help and support
 
-## [![](https://img.shields.io/badge/GitHub%20Pages-https://caravagnalab.github.io/TAPACLOTH/-yellow.svg)](https://caravagnalab.github.io/TAPACLOTH)
+## [![](https://img.shields.io/badge/GitHub%20Pages-https://caravagnalab.github.io/INCOMMON/-yellow.svg)](https://caravagnalab.github.io/INCOMMON)
 
 ## Installation
 
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 06262a5..1c1fbf9 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,4 +1,4 @@
-url: caravagnalab.github.io/TAPACLOTH
+url: caravagnalab.github.io/INCOMMON
 template:
   bootstrap: 5
 
diff --git a/data/example_data.rda b/data/example_data.rda
index 934ecd6..b189d43 100644
Binary files a/data/example_data.rda and b/data/example_data.rda differ
diff --git a/data/pcawg_priors.rda b/data/pcawg_priors.rda
new file mode 100644
index 0000000..b0e5a7a
Binary files /dev/null and b/data/pcawg_priors.rda differ
diff --git a/docs/404.html b/docs/404.html
index 80af188..6d642c8 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -5,31 +5,31 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<title>Page not found (404) • TAPACLOTH</title>
-<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="caravagnalab.github.io/TAPACLOTH/favicon-16x16.png">
-<link rel="icon" type="image/png" sizes="32x32" href="caravagnalab.github.io/TAPACLOTH/favicon-32x32.png">
-<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="caravagnalab.github.io/TAPACLOTH/apple-touch-icon.png">
-<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="caravagnalab.github.io/TAPACLOTH/apple-touch-icon-120x120.png">
-<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="caravagnalab.github.io/TAPACLOTH/apple-touch-icon-76x76.png">
-<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="caravagnalab.github.io/TAPACLOTH/apple-touch-icon-60x60.png">
-<script src="caravagnalab.github.io/TAPACLOTH/deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<link href="caravagnalab.github.io/TAPACLOTH/deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet">
-<script src="caravagnalab.github.io/TAPACLOTH/deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<title>Page not found (404) • INCOMMON</title>
+<!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="caravagnalab.github.io/INCOMMON/favicon-16x16.png">
+<link rel="icon" type="image/png" sizes="32x32" href="caravagnalab.github.io/INCOMMON/favicon-32x32.png">
+<link rel="apple-touch-icon" type="image/png" sizes="180x180" href="caravagnalab.github.io/INCOMMON/apple-touch-icon.png">
+<link rel="apple-touch-icon" type="image/png" sizes="120x120" href="caravagnalab.github.io/INCOMMON/apple-touch-icon-120x120.png">
+<link rel="apple-touch-icon" type="image/png" sizes="76x76" href="caravagnalab.github.io/INCOMMON/apple-touch-icon-76x76.png">
+<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="caravagnalab.github.io/INCOMMON/apple-touch-icon-60x60.png">
+<script src="caravagnalab.github.io/INCOMMON/deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
+<link href="caravagnalab.github.io/INCOMMON/deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="caravagnalab.github.io/INCOMMON/deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
 <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
-<!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="caravagnalab.github.io/TAPACLOTH/pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
-<meta property="og:image" content="caravagnalab.github.io/TAPACLOTH/logo.png">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="caravagnalab.github.io/INCOMMON/pkgdown.js"></script><meta property="og:title" content="Page not found (404)">
+<meta property="og:image" content="caravagnalab.github.io/INCOMMON/logo.png">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]-->
 </head>
 <body>
-    <a href="caravagnalab.github.io/TAPACLOTH/#main" class="visually-hidden-focusable">Skip to contents</a>
+    <a href="caravagnalab.github.io/INCOMMON/#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
     <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
     
-    <a class="navbar-brand me-2" href="caravagnalab.github.io/TAPACLOTH/index.html">TAPACLOTH</a>
+    <a class="navbar-brand me-2" href="caravagnalab.github.io/INCOMMON/index.html">INCOMMON</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1</small>
 
@@ -41,16 +41,15 @@
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
 <li class="nav-item">
-  <a class="nav-link" href="caravagnalab.github.io/TAPACLOTH/articles/TAPACLOTH.html">Get started</a>
+  <a class="nav-link" href="caravagnalab.github.io/INCOMMON/articles/INCOMMON.html">Get started</a>
 </li>
 <li class="nav-item">
-  <a class="nav-link" href="caravagnalab.github.io/TAPACLOTH/reference/index.html">Reference</a>
+  <a class="nav-link" href="caravagnalab.github.io/INCOMMON/reference/index.html">Reference</a>
 </li>
 <li class="nav-item dropdown">
-  <a href="caravagnalab.github.io/TAPACLOTH/#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
+  <a href="caravagnalab.github.io/INCOMMON/#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="caravagnalab.github.io/TAPACLOTH/articles/classify-and-plot.html">Classify karyotype and multiplicity</a>
-    <a class="dropdown-item" href="caravagnalab.github.io/TAPACLOTH/articles/purity-estimates.html">Purity estimates</a>
+    <a class="dropdown-item" href="caravagnalab.github.io/INCOMMON/articles/Classify_Mutations.html">Classify mutations from a targeted sequencing sample</a>
   </div>
 </li>
       </ul>
@@ -60,7 +59,7 @@
 
       <ul class="navbar-nav">
 <li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/caravagnalab/TAPACLOTH/" aria-label="github">
+  <a class="external-link nav-link" href="https://github.com/caravagnalab/INCOMMON/" aria-label="github">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -73,7 +72,7 @@
 </nav><div class="container template-title-body">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="caravagnalab.github.io/TAPACLOTH/logo.png" class="logo" alt=""><h1>Page not found (404)</h1>
+      <img src="caravagnalab.github.io/INCOMMON/logo.png" class="logo" alt=""><h1>Page not found (404)</h1>
       
     </div>
 
@@ -90,7 +89,7 @@
 
 <div class="pkgdown-footer-right">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer>
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 6f42aa5..1e0483e 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • TAPACLOTH</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"><meta property="og:image" content="caravagnalab.github.io/TAPACLOTH/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>License • INCOMMON</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="License"><meta property="og:image" content="caravagnalab.github.io/INCOMMON/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -8,7 +8,7 @@
 
     <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
     
-    <a class="navbar-brand me-2" href="index.html">TAPACLOTH</a>
+    <a class="navbar-brand me-2" href="index.html">INCOMMON</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1</small>
 
@@ -19,7 +19,7 @@
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="articles/TAPACLOTH.html">Get started</a>
+  <a class="nav-link" href="articles/INCOMMON.html">Get started</a>
 </li>
 <li class="nav-item">
   <a class="nav-link" href="reference/index.html">Reference</a>
@@ -27,15 +27,14 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="articles/classify-and-plot.html">Classify karyotype and multiplicity</a>
-    <a class="dropdown-item" href="articles/purity-estimates.html">Purity estimates</a>
+    <a class="dropdown-item" href="articles/Classify_Mutations.html">Classify mutations from a targeted sequencing sample</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
       <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/caravagnalab/TAPACLOTH/" aria-label="github">
+  <a class="external-link nav-link" href="https://github.com/caravagnalab/INCOMMON/" aria-label="github">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -52,7 +51,7 @@
     </div>
 
 <pre>YEAR: 2022
-COPYRIGHT HOLDER: TAPACLOTH authors
+COPYRIGHT HOLDER: INCOMMON authors
 </pre>
 
   </main></div>
@@ -63,7 +62,7 @@
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
index d60a654..5a6cfb7 100644
--- a/docs/LICENSE.html
+++ b/docs/LICENSE.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>GNU General Public License • INCOMMON</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="GNU General Public License"><meta property="og:image" content="caravagnalab.github.io/INCOMMON/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
@@ -8,7 +8,7 @@
 
     <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
     
-    <a class="navbar-brand me-2" href="index.html">TAPACLOTH</a>
+    <a class="navbar-brand me-2" href="index.html">INCOMMON</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1</small>
 
@@ -19,7 +19,7 @@
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="articles/TAPACLOTH.html">Get started</a>
+  <a class="nav-link" href="articles/INCOMMON.html">Get started</a>
 </li>
 <li class="nav-item">
   <a class="nav-link" href="reference/index.html">Reference</a>
@@ -27,15 +27,14 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="articles/classify-and-plot.html">Classify karyotype and multiplicity</a>
-    <a class="dropdown-item" href="articles/purity-estimates.html">Purity estimates</a>
+    <a class="dropdown-item" href="articles/Classify_Mutations.html">Classify mutations from a targeted sequencing sample</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
       <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/caravagnalab/TAPACLOTH/" aria-label="github">
+  <a class="external-link nav-link" href="https://github.com/caravagnalab/INCOMMON/" aria-label="github">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -48,7 +47,7 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="logo.png" class="logo" alt=""><h1>GNU General Public License</h1>
-      <small class="dont-index">Source: <a href="https://github.com/caravagnalab/TAPACLOTH/blob/HEAD/LICENSE.md" class="external-link"><code>LICENSE.md</code></a></small>
+      <small class="dont-index">Source: <a href="https://github.com/caravagnalab/INCOMMON/blob/HEAD/LICENSE.md" class="external-link"><code>LICENSE.md</code></a></small>
     </div>
 
 <div id="gnu-general-public-license" class="section level1">
@@ -221,27 +220,27 @@ <h3 id="id_17-interpretation-of-sections-15-and-16">17. Interpretation of Sectio
 <h2 id="how-to-apply-these-terms-to-your-new-programs">How to Apply These Terms to Your New Programs<a class="anchor" aria-label="anchor" href="#how-to-apply-these-terms-to-your-new-programs"></a></h2>
 <p>If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.</p>
 <p>To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively state the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.</p>
-<div class="sourceCode" id="cb1"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="sc">&lt;</span>one line to give the program<span class="st">'s name and a brief idea of what it does.&gt;</span></span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="st">Copyright (C) &lt;year&gt;  &lt;name of author&gt;</span></span>
-<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="st">This program is free software: you can redistribute it and/or modify</span></span>
-<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="st">it under the terms of the GNU General Public License as published by</span></span>
-<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="st">the Free Software Foundation, either version 3 of the License, or</span></span>
-<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="st">(at your option) any later version.</span></span>
-<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="st">This program is distributed in the hope that it will be useful,</span></span>
-<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="st">but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
-<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="st">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span></span>
-<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="st">GNU General Public License for more details.</span></span>
-<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="st">You should have received a copy of the GNU General Public License</span></span>
-<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="st">along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span></span></code></pre></div>
+<div class="sourceCode" id="cb1"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a><span class="sc">&lt;</span>one line to give the program<span class="st">'s name and a brief idea of what it does.&gt;</span></span>
+<span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a><span class="st">Copyright (C) &lt;year&gt;  &lt;name of author&gt;</span></span>
+<span id="cb1-3"><a href="#cb1-3" tabindex="-1"></a></span>
+<span id="cb1-4"><a href="#cb1-4" tabindex="-1"></a><span class="st">This program is free software: you can redistribute it and/or modify</span></span>
+<span id="cb1-5"><a href="#cb1-5" tabindex="-1"></a><span class="st">it under the terms of the GNU General Public License as published by</span></span>
+<span id="cb1-6"><a href="#cb1-6" tabindex="-1"></a><span class="st">the Free Software Foundation, either version 3 of the License, or</span></span>
+<span id="cb1-7"><a href="#cb1-7" tabindex="-1"></a><span class="st">(at your option) any later version.</span></span>
+<span id="cb1-8"><a href="#cb1-8" tabindex="-1"></a></span>
+<span id="cb1-9"><a href="#cb1-9" tabindex="-1"></a><span class="st">This program is distributed in the hope that it will be useful,</span></span>
+<span id="cb1-10"><a href="#cb1-10" tabindex="-1"></a><span class="st">but WITHOUT ANY WARRANTY; without even the implied warranty of</span></span>
+<span id="cb1-11"><a href="#cb1-11" tabindex="-1"></a><span class="st">MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span></span>
+<span id="cb1-12"><a href="#cb1-12" tabindex="-1"></a><span class="st">GNU General Public License for more details.</span></span>
+<span id="cb1-13"><a href="#cb1-13" tabindex="-1"></a></span>
+<span id="cb1-14"><a href="#cb1-14" tabindex="-1"></a><span class="st">You should have received a copy of the GNU General Public License</span></span>
+<span id="cb1-15"><a href="#cb1-15" tabindex="-1"></a><span class="st">along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</span></span></code></pre></div>
 <p>Also add information on how to contact you by electronic and paper mail.</p>
 <p>If the program does terminal interaction, make it output a short notice like this when it starts in an interactive mode:</p>
-<div class="sourceCode" id="cb2"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="sc">&lt;</span>program<span class="sc">&gt;</span>  <span class="fu">Copyright</span> (C) <span class="sc">&lt;</span>year<span class="sc">&gt;</span>  <span class="er">&lt;</span>name of author<span class="sc">&gt;</span></span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>This program comes with ABSOLUTELY NO WARRANTY; <span class="cf">for</span> details type <span class="st">'show w'</span>.</span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>This is free software, and you are welcome to redistribute it</span>
-<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>under certain conditions; type <span class="st">'show c'</span> <span class="cf">for</span> details.</span></code></pre></div>
+<div class="sourceCode" id="cb2"><pre class="sourceCode R"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="sc">&lt;</span>program<span class="sc">&gt;</span>  <span class="fu">Copyright</span> (C) <span class="sc">&lt;</span>year<span class="sc">&gt;</span>  <span class="er">&lt;</span>name of author<span class="sc">&gt;</span></span>
+<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a>This program comes with ABSOLUTELY NO WARRANTY; <span class="cf">for</span> details type <span class="st">'show w'</span>.</span>
+<span id="cb2-3"><a href="#cb2-3" tabindex="-1"></a>This is free software, and you are welcome to redistribute it</span>
+<span id="cb2-4"><a href="#cb2-4" tabindex="-1"></a>under certain conditions; type <span class="st">'show c'</span> <span class="cf">for</span> details.</span></code></pre></div>
 <p>The hypothetical commands <code>show w</code> and <code>show c</code> should show the appropriate parts of the General Public License. Of course, your program’s commands might be different; for a GUI interface, you would use an “about box”.</p>
 <p>You should also get your employer (if you work as a programmer) or school, if any, to sign a “copyright disclaimer” for the program, if necessary. For more information on this, and how to apply and follow the GNU GPL, see &lt;<a href="http://www.gnu.org/licenses/" class="external-link uri">http://www.gnu.org/licenses/</a>&gt;.</p>
 <p>The GNU General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. But first, please read &lt;<a href="http://www.gnu.org/philosophy/why-not-lgpl.html" class="external-link uri">http://www.gnu.org/philosophy/why-not-lgpl.html</a>&gt;.</p>
@@ -257,7 +256,7 @@ <h2 id="how-to-apply-these-terms-to-your-new-programs">How to Apply These Terms
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 8707d3f..3c7729a 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • TAPACLOTH</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="caravagnalab.github.io/TAPACLOTH/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Articles • INCOMMON</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Articles"><meta property="og:image" content="caravagnalab.github.io/INCOMMON/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -8,7 +8,7 @@
 
     <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
     
-    <a class="navbar-brand me-2" href="../index.html">TAPACLOTH</a>
+    <a class="navbar-brand me-2" href="../index.html">INCOMMON</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1</small>
 
@@ -19,7 +19,7 @@
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/TAPACLOTH.html">Get started</a>
+  <a class="nav-link" href="../articles/INCOMMON.html">Get started</a>
 </li>
 <li class="nav-item">
   <a class="nav-link" href="../reference/index.html">Reference</a>
@@ -27,15 +27,14 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/classify-and-plot.html">Classify karyotype and multiplicity</a>
-    <a class="dropdown-item" href="../articles/purity-estimates.html">Purity estimates</a>
+    <a class="dropdown-item" href="../articles/Classify_Mutations.html">Classify mutations from a targeted sequencing sample</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
       <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/caravagnalab/TAPACLOTH/" aria-label="github">
+  <a class="external-link nav-link" href="https://github.com/caravagnalab/INCOMMON/" aria-label="github">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -54,11 +53,9 @@
       <h3>All vignettes</h3>
       <p class="section-desc"></p>
 
-      <dl><dt><a href="TAPACLOTH.html">TAPACLOTH</a></dt>
+      <dl><dt><a href="Classify_Mutations.html">Classify mutations from a targeted sequencing sample</a></dt>
         <dd>
-        </dd><dt><a href="classify-and-plot.html">Classify karyotype and multiplicity</a></dt>
-        <dd>
-        </dd><dt><a href="purity-estimates.html">Purity estimates</a></dt>
+        </dd><dt><a href="INCOMMON.html">INCOMMON</a></dt>
         <dd>
       </dd></dl></div>
   </main></div>
@@ -69,7 +66,7 @@ <h3>All vignettes</h3>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
diff --git a/docs/authors.html b/docs/authors.html
index 03f43ee..799262b 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • TAPACLOTH</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.1.3/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><meta property="og:image" content="caravagnalab.github.io/TAPACLOTH/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Authors and Citation • INCOMMON</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png"><script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Authors and Citation"><meta property="og:image" content="caravagnalab.github.io/INCOMMON/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -8,7 +8,7 @@
 
     <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
     
-    <a class="navbar-brand me-2" href="index.html">TAPACLOTH</a>
+    <a class="navbar-brand me-2" href="index.html">INCOMMON</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1</small>
 
@@ -19,7 +19,7 @@
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="articles/TAPACLOTH.html">Get started</a>
+  <a class="nav-link" href="articles/INCOMMON.html">Get started</a>
 </li>
 <li class="nav-item">
   <a class="nav-link" href="reference/index.html">Reference</a>
@@ -27,15 +27,14 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="articles/classify-and-plot.html">Classify karyotype and multiplicity</a>
-    <a class="dropdown-item" href="articles/purity-estimates.html">Purity estimates</a>
+    <a class="dropdown-item" href="articles/Classify_Mutations.html">Classify mutations from a targeted sequencing sample</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
       <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/caravagnalab/TAPACLOTH/" aria-label="github">
+  <a class="external-link nav-link" href="https://github.com/caravagnalab/INCOMMON/" aria-label="github">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -65,18 +64,18 @@ <h2>Authors</h2>
 
     <div class="section level2 citation">
       <h2 id="citation">Citation</h2>
-      <p><small class="dont-index">Source: <a href="https://github.com/caravagnalab/TAPACLOTH/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
+      <p><small class="dont-index">Source: <a href="https://github.com/caravagnalab/INCOMMON/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
 
-      <p>Calonaci N, Caravagna G (2022).
-<em>TAPACLOTH: Targeted panel-oriented test for clonality and heterozygosity</em>.
-R package version 0.0.1, <a href="https://github.com/caravagnalab/TAPACLOTH" class="external-link">https://github.com/caravagnalab/TAPACLOTH</a>. 
+      <p>Calonaci N, Caravagna G (2024).
+<em>INCOMMON: Targeted panel-oriented test for clonality and heterozygosity</em>.
+R package version 0.0.1, <a href="https://github.com/caravagnalab/INCOMMON" class="external-link">https://github.com/caravagnalab/INCOMMON</a>. 
 </p>
       <pre>@Manual{,
-  title = {TAPACLOTH: Targeted panel-oriented test for clonality and heterozygosity},
+  title = {INCOMMON: Targeted panel-oriented test for clonality and heterozygosity},
   author = {Nicola Calonaci and Giulio Caravagna},
-  year = {2022},
+  year = {2024},
   note = {R package version 0.0.1},
-  url = {https://github.com/caravagnalab/TAPACLOTH},
+  url = {https://github.com/caravagnalab/INCOMMON},
 }</pre>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -88,7 +87,7 @@ <h2 id="citation">Citation</h2>
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
diff --git a/docs/index.html b/docs/index.html
index bedd230..86ec23e 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -5,12 +5,13 @@
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge">
 <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-<meta name="description" content="TAPACLOTH is a tool that classifies somatic mutation calls from
-    targeted-panel sequencing as either subclonal, clonal heterozygous or clonal 
-    LOH thorugh a statistical hypothesis test based on a Binomial or Beta-Binomial 
-    modelling of the sequencing read count process. As an additional feature, 
-    TAPACLOTH can be used to infer sample purity.">
-<title>Targeted panel-oriented test for clonality and heterozygosity • TAPACLOTH</title>
+<meta name="description" content="INCOMMON is a tool for the INference of COpy number and Mutation Multiplicity in ONcology. 
+            INCOMMON infers the copy number and multiplicity of somatic mutations from tumour-only read count data, 
+            and can be applied to classify mutations from large-size datasets in an efficient and fast way.
+            Mutations are classified as either Tier-1 (present in 100% cells) without copy-number alterations 
+            (heterozygous mutant diploid HMD), with loss of heterozygosity (LOH), copy-neutral LOH (CNLOH), amplification (AM), 
+            or Tier-2 (subclonal or with high ploidy and low multiplicity).">
+<title>Targeted panel-oriented test for clonality and heterozygosity • INCOMMON</title>
 <!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="favicon-16x16.png">
 <link rel="icon" type="image/png" sizes="32x32" href="favicon-32x32.png">
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@@ -18,16 +19,17 @@
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 <link rel="apple-touch-icon" type="image/png" sizes="60x60" href="apple-touch-icon-60x60.png">
 <script src="deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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-<script src="deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
+<link href="deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet">
+<script src="deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
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-<!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Targeted panel-oriented test for clonality and heterozygosity">
-<meta property="og:description" content="TAPACLOTH is a tool that classifies somatic mutation calls from
-    targeted-panel sequencing as either subclonal, clonal heterozygous or clonal 
-    LOH thorugh a statistical hypothesis test based on a Binomial or Beta-Binomial 
-    modelling of the sequencing read count process. As an additional feature, 
-    TAPACLOTH can be used to infer sample purity.">
-<meta property="og:image" content="caravagnalab.github.io/TAPACLOTH/logo.png">
+<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="pkgdown.js"></script><meta property="og:title" content="Targeted panel-oriented test for clonality and heterozygosity">
+<meta property="og:description" content="INCOMMON is a tool for the INference of COpy number and Mutation Multiplicity in ONcology. 
+            INCOMMON infers the copy number and multiplicity of somatic mutations from tumour-only read count data, 
+            and can be applied to classify mutations from large-size datasets in an efficient and fast way.
+            Mutations are classified as either Tier-1 (present in 100% cells) without copy-number alterations 
+            (heterozygous mutant diploid HMD), with loss of heterozygosity (LOH), copy-neutral LOH (CNLOH), amplification (AM), 
+            or Tier-2 (subclonal or with high ploidy and low multiplicity).">
+<meta property="og:image" content="caravagnalab.github.io/INCOMMON/logo.png">
 <!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -39,7 +41,7 @@
 
     <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
     
-    <a class="navbar-brand me-2" href="index.html">TAPACLOTH</a>
+    <a class="navbar-brand me-2" href="index.html">INCOMMON</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1</small>
 
@@ -51,7 +53,7 @@
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto">
 <li class="nav-item">
-  <a class="nav-link" href="articles/TAPACLOTH.html">Get started</a>
+  <a class="nav-link" href="articles/INCOMMON.html">Get started</a>
 </li>
 <li class="nav-item">
   <a class="nav-link" href="reference/index.html">Reference</a>
@@ -59,8 +61,7 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="articles/classify-and-plot.html">Classify karyotype and multiplicity</a>
-    <a class="dropdown-item" href="articles/purity-estimates.html">Purity estimates</a>
+    <a class="dropdown-item" href="articles/Classify_Mutations.html">Classify mutations from a targeted sequencing sample</a>
   </div>
 </li>
       </ul>
@@ -70,7 +71,7 @@
 
       <ul class="navbar-nav">
 <li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/caravagnalab/TAPACLOTH/" aria-label="github">
+  <a class="external-link nav-link" href="https://github.com/caravagnalab/INCOMMON/" aria-label="github">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -84,29 +85,29 @@
 <div class="row">
   <main id="main" class="col-md-9"><div class="section level1">
 <div class="page-header">
-<img src="logo.png" class="logo" alt=""><h1 id="tapacloth-">TAPACLOTH 
-<a class="anchor" aria-label="anchor" href="#tapacloth-"></a>
+<img src="logo.png" class="logo" alt=""><h1 id="incommon-">INCOMMON 
+<a class="anchor" aria-label="anchor" href="#incommon-"></a>
 </h1>
 </div>
 <!-- badges: start -->
 
-<p>TAPACLOTH is a tool that uses targeted sequencing data to classify somatic mutations as either subclonal, clonal heterozygous or clonal with loss of heterozygosity. Two types of tests are available: an exact one based on Binomial or Beta-Binomial modelling of sequencing read counts, and approximate based on allelic frequencies. The former is parametrised by a p-value. Additionally, TAPACLOTH can infer sample purity, an information used to carry out variant classification. Since the two tests are independent, one can first estimate sample purity and then use it as input for the classification task.</p>
+<p>INCOMMON is a tool for the INference of COpy number and Mutation Multiplicity in ONcology. INCOMMON infers the copy number and multiplicity of somatic mutations from tumour-only read count data, and can applied to classify mutations from large-size datasets in an efficient and fast way. Mutations are classified as either Tier-1 (present in 100% cells) without copy-number alterations (heterozygous mutant diploid HMD), with loss of heterozygosity (LOH), copy-neutral LOH (CNLOH), amplification (AM), or Tier-2 (subclonal or with high ploidy and low multiplicity).</p>
 <div class="section level4">
 <h4 id="help-and-support">Help and support<a class="anchor" aria-label="anchor" href="#help-and-support"></a>
 </h4>
 </div>
 <div class="section level2">
 <h2 id="section">
-<a href="https://caravagnalab.github.io/TAPACLOTH"><img src="https://img.shields.io/badge/GitHub%20Pages-https://caravagnalab.github.io/TAPACLOTH/-yellow.svg"></a><a class="anchor" aria-label="anchor" href="#section"></a>
+<a href="https://caravagnalab.github.io/INCOMMON"><img src="https://img.shields.io/badge/GitHub%20Pages-https://caravagnalab.github.io/INCOMMON/-yellow.svg"></a><a class="anchor" aria-label="anchor" href="#section"></a>
 </h2>
 </div>
 <div class="section level2">
 <h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
 </h2>
-<p>You can install the development version of TAPACLOTH from <a href="https://github.com/" class="external-link">GitHub</a> with:</p>
+<p>You can install the development version of INCOMMON from <a href="https://github.com/" class="external-link">GitHub</a> with:</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># install.packages("devtools")</span></span>
-<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"caravagnalab/TAPACLOTH"</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"caravagnalab/INCOMMON"</span><span class="op">)</span></span></code></pre></div>
 <div class="section level4">
 <h4 id="copyright-and-contacts">Copyright and contacts<a class="anchor" aria-label="anchor" href="#copyright-and-contacts"></a>
 </h4>
@@ -118,8 +119,8 @@ <h4 id="copyright-and-contacts">Copyright and contacts<a class="anchor" aria-lab
   </main><aside class="col-md-3"><div class="links">
 <h2 data-toc-skip>Links</h2>
 <ul class="list-unstyled">
-<li><a href="https://github.com/caravagnalab/TAPACLOTH/" class="external-link">Browse source code</a></li>
-<li><a href="https://github.com/caravagnalab/TAPACLOTH/issues" class="external-link">Report a bug</a></li>
+<li><a href="https://github.com/caravagnalab/INCOMMON/" class="external-link">Browse source code</a></li>
+<li><a href="https://github.com/caravagnalab/INCOMMON/issues" class="external-link">Report a bug</a></li>
 </ul>
 </div>
 
@@ -135,7 +136,7 @@ <h2 data-toc-skip>License</h2>
 <div class="citation">
 <h2 data-toc-skip>Citation</h2>
 <ul class="list-unstyled">
-<li><a href="authors.html#citation">Citing TAPACLOTH</a></li>
+<li><a href="authors.html#citation">Citing INCOMMON</a></li>
 </ul>
 </div>
 
@@ -150,7 +151,7 @@ <h2 data-toc-skip>Developers</h2>
 <div class="dev-status">
 <h2 data-toc-skip>Dev status</h2>
 <ul class="list-unstyled">
-<li><a href="https://github.com/caravagnalab/TAPACLOTH/actions/workflows/R-CMD-check.yaml" class="external-link"><img src="https://github.com/caravagnalab/TAPACLOTH/actions/workflows/R-CMD-check.yaml/badge.svg" alt="R-CMD-check"></a></li>
+<li><a href="https://github.com/caravagnalab/INCOMMON/actions/workflows/R-CMD-check.yaml" class="external-link"><img src="https://github.com/caravagnalab/INCOMMON/actions/workflows/R-CMD-check.yaml/badge.svg" alt="R-CMD-check"></a></li>
 </ul>
 </div>
 
@@ -165,7 +166,7 @@ <h2 data-toc-skip>Dev status</h2>
 
 <div class="pkgdown-footer-right">
   <p></p>
-<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer>
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 74fd73c..ffe9204 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -1,12 +1,11 @@
-pandoc: '2.18'
-pkgdown: 2.0.6
+pandoc: 3.1.1
+pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
-  TAPACLOTH: TAPACLOTH.html
-  classify-and-plot: classify-and-plot.html
-  purity-estimates: purity-estimates.html
-last_built: 2022-09-05T07:20Z
+  Classify_Mutations: Classify_Mutations.html
+  INCOMMON: INCOMMON.html
+last_built: 2024-03-15T18:14Z
 urls:
-  reference: caravagnalab.github.io/TAPACLOTH/reference
-  article: caravagnalab.github.io/TAPACLOTH/articles
+  reference: caravagnalab.github.io/INCOMMON/reference
+  article: caravagnalab.github.io/INCOMMON/articles
 
diff --git a/docs/reference/estimate_purity.html b/docs/reference/estimate_purity.html
index 57657f9..ec98157 100644
--- a/docs/reference/estimate_purity.html
+++ b/docs/reference/estimate_purity.html
@@ -1,5 +1,5 @@
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@@ -90,47 +90,11 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">input</span> <span class="op">=</span> <span class="fu"><a href="init.html">init</a></span><span class="op">(</span>mutations <span class="op">=</span> <span class="va">example_data</span><span class="op">$</span><span class="va">data</span>, sample <span class="op">=</span> <span class="va">example_data</span><span class="op">$</span><span class="va">sample</span>, purity <span class="op">=</span> <span class="va">example_data</span><span class="op">$</span><span class="va">purity</span><span class="op">)</span></span></span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in left_join(mutations, gene_roles, by = "gene"):</span> could not find function "left_join"</span>
 <span class="r-in"><span><span class="va">out</span> <span class="op">=</span> <span class="fu">estimate_purity</span><span class="op">(</span>x <span class="op">=</span> <span class="va">input</span>, model <span class="op">=</span> <span class="st">"binomial"</span>, eps <span class="op">=</span> <span class="fl">0.01</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">TAPACLOTH purity estimate of sample </span><span style="color: #00BB00; font-weight: bold;">P-0050275-T01-IM6</span><span style="font-weight: bold;"> using </span><span style="color: #00BB00; font-weight: bold;">binomial</span><span style="font-weight: bold;"> model</span> <span style="color: #00BBBB;">──</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">BMix fit</span> <span style="color: #00BBBB;">────────────────────────────────────────────────────────────────────</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Binomials k_B = <span style="color: #00BB00;">1</span>, <span style="color: #00BB00;">2</span>, and <span style="color: #00BB00;">3</span>, Beta-Binomials k_BB = <span style="color: #00BB00;">0</span>; 6 fits to run.</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> <span style="font-weight: bold;">Bmix best fit</span> completed in 0 mins</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="color: #000000; background-color: #BBBB00;">[ BMix ] My BMix model</span> n = 10 with <span style="color: #00BB00;">k = 3</span> component(s) (<span style="color: #00BB00;">3</span> + <span style="color: #00BB00;">0</span>) ───────────────</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • Clusters: π = 40% [<span style="color: #BBBB00;">Bin 1</span>], 40% [<span style="color: #BBBB00;">Bin 3</span>], and 20% [<span style="color: #BBBB00;">Bin 2</span>], with π &gt; 0.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • Binomial <span style="color: #00BB00;">Bin 1</span> with mean = 0.45359630436383.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • Binomial <span style="color: #00BB00;">Bin 2</span> with mean = 0.565008987772999.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> • Binomial <span style="color: #00BB00;">Bin 3</span> with mean = 0.214805305947763.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Score (model selection): <span style="color: #00BB00;">ICL</span> = 149.86.</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>`guides(&lt;scale&gt; = FALSE)` is deprecated. Please use `guides(&lt;scale&gt; = "none")` instead.</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values (geom_bar).</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Graphs cannot be horizontally aligned unless the axis parameter is set. Placing graphs unaligned.</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in estimate_purity(x = input, model = "binomial", eps = 0.01):</span> unused argument (model = "binomial")</span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="color: #000000; background-color: #BB00BB;">[ TAPACLOTH ] </span> Input data for sample <span style="color: #00BB00;">P-0050275-T01-IM6</span>, with purity <span style="color: #00BB00;">0.9</span> ─────</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 10 × 10</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    chr        from        to ref   alt   gene      NV    DP   VAF gene_role     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>         </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> chr17   7<span style="text-decoration: underline;">578</span>542   7<span style="text-decoration: underline;">578</span>542 C     G     TP53     397   850 0.467 oncogene, TSG…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> chr12  25<span style="text-decoration: underline;">380</span>275  25<span style="text-decoration: underline;">380</span>275 A     C     KRAS     634  <span style="text-decoration: underline;">1</span>121 0.566 oncogene      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> chr9   21<span style="text-decoration: underline;">971</span>120  21<span style="text-decoration: underline;">971</span>120 C     T     CDKN2A   389   866 0.449 TSG           </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> chr9   21<span style="text-decoration: underline;">971</span>120  21<span style="text-decoration: underline;">971</span>120 C     T     CDKN2A   389   866 0.449 TSG           </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> chr1   27<span style="text-decoration: underline;">105</span>553  27<span style="text-decoration: underline;">105</span>553 C     T     ARID1A   309   548 0.564 TSG, fusion   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> chr9   21<span style="text-decoration: underline;">971</span>120  21<span style="text-decoration: underline;">971</span>120 C     T     CDKN2A   389   866 0.449 TSG           </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> chr1   46<span style="text-decoration: underline;">724</span>370  46<span style="text-decoration: underline;">724</span>370 C     T     RAD54L    76   520 0.146 <span style="color: #BB0000;">NA</span>            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> chr17  30<span style="text-decoration: underline;">315</span>354  30<span style="text-decoration: underline;">315</span>354 G     A     SUZ12     93   542 0.172 oncogene, TSG…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> chr2  158<span style="text-decoration: underline;">622</span>618 158<span style="text-decoration: underline;">622</span>618 A     G     ACVR1    175   616 0.284 oncogene      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> chr6     <span style="text-decoration: underline;">394</span>875    <span style="text-decoration: underline;">394</span>875 C     T     IRF4     158   659 0.240 oncogene, TSG…</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="color: #000000; background-color: #BB00BB;">[ TAPACLOTH ] </span> Purity estimate using  <span style="color: #000000; background-color: #BBBB00;">[ BMix ] </span> with <span style="color: #00BB00;">binomial</span> model ─────────</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 3</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   purity reliability purity_bmix</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span>    0.9       0.989        0.91</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in print(out):</span> object 'out' not found</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -142,7 +106,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
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index 36b4713..5dd1d8b 100644
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@@ -1,5 +1,5 @@
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+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Function reference • INCOMMON</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Function reference"><meta property="og:image" content="caravagnalab.github.io/INCOMMON/logo.png"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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 <![endif]--></head><body>
@@ -8,7 +8,7 @@
 
     <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
     
-    <a class="navbar-brand me-2" href="../index.html">TAPACLOTH</a>
+    <a class="navbar-brand me-2" href="../index.html">INCOMMON</a>
 
     <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.0.1</small>
 
@@ -19,7 +19,7 @@
 
     <div id="navbar" class="collapse navbar-collapse ms-3">
       <ul class="navbar-nav me-auto"><li class="nav-item">
-  <a class="nav-link" href="../articles/TAPACLOTH.html">Get started</a>
+  <a class="nav-link" href="../articles/INCOMMON.html">Get started</a>
 </li>
 <li class="active nav-item">
   <a class="nav-link" href="../reference/index.html">Reference</a>
@@ -27,15 +27,14 @@
 <li class="nav-item dropdown">
   <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-articles">Articles</a>
   <div class="dropdown-menu" aria-labelledby="dropdown-articles">
-    <a class="dropdown-item" href="../articles/classify-and-plot.html">Classify karyotype and multiplicity</a>
-    <a class="dropdown-item" href="../articles/purity-estimates.html">Purity estimates</a>
+    <a class="dropdown-item" href="../articles/Classify_Mutations.html">Classify mutations from a targeted sequencing sample</a>
   </div>
 </li>
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
       <ul class="navbar-nav"><li class="nav-item">
-  <a class="external-link nav-link" href="https://github.com/caravagnalab/TAPACLOTH/" aria-label="github">
+  <a class="external-link nav-link" href="https://github.com/caravagnalab/INCOMMON/" aria-label="github">
     <span class="fab fa fab fa-github fa-lg"></span>
      
   </a>
@@ -63,109 +62,44 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 
       <dl><dt>
           
-          <code><a href="binomial_test.html">binomial_test()</a></code> 
+          <code><a href="classification.html">classification()</a></code> 
         </dt>
-        <dd>Compute likelihoods and uncertainty..</dd>
+        <dd>Getter for class <code>'INCOMMON'</code>.</dd>
       </dl><dl><dt>
           
-          <code><a href="estimate_purity.html">estimate_purity()</a></code> 
+          <code><a href="classify.html">classify()</a></code> 
         </dt>
-        <dd>Infer sample purity using a mixture of Binomial or Beta-Binomial distributions.</dd>
+        <dd>Classify mutations using a Beta-Binomial model-based test.</dd>
       </dl><dl><dt>
           
-          <code><a href="gene_classification.html">gene_classification()</a></code> 
+          <code><a href="compute_posterior.html">compute_posterior()</a></code> 
         </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_DP.html">get_DP()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_NV.html">get_NV()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_VAF.html">get_VAF()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_classes.html">get_classes()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_classifier.html">get_classifier()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_coord.html">get_coord()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_gene.html">get_gene()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_id.html">get_id()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_params.html">get_params()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_purity_bmix.html">get_purity_bmix()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_purity_estimate.html">get_purity_estimate()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="get_reliability.html">get_reliability()</a></code> 
-        </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
+        <dd>Compute model likelihood, posterior and entropy</dd>
       </dl><dl><dt>
           
           <code><a href="init.html">init()</a></code> 
         </dt>
-        <dd>Prepare input for analyses with <code>'TAPACLOTH'</code>.</dd>
+        <dd>Prepare input for analyses with <code>'INCOMMON'</code>.</dd>
       </dl><dl><dt>
           
-          <code><a href="models_avail.html">models_avail()</a></code> 
+          <code><a href="parameters.html">parameters()</a></code> 
         </dt>
-        <dd>Getter for class <code>'TAPACLOTH'</code>.</dd>
+        <dd>Getter for class <code>'INCOMMON'</code>.</dd>
       </dl><dl><dt>
           
-          <code><a href="plot.TAPACLOTH.html">plot.TAPACLOTH()</a></code> 
+          <code><a href="plot.INCOMMON.html">plot(<i>&lt;INCOMMON&gt;</i>)</a></code> 
         </dt>
-        <dd>Plot for class <code>'TAPACLOTH'</code>.</dd>
+        <dd>Plot for class <code>'INCOMMON'</code>.</dd>
       </dl><dl><dt>
           
-          <code><a href="plot_bmix.html">plot_bmix()</a></code> 
+          <code><a href="plot_classification.html">plot_classification()</a></code> 
         </dt>
-        <dd>Plot function for class <code>'TAPACLOTH'</code>.</dd>
+        <dd>Visualize classification results for individual observations.</dd>
       </dl><dl><dt>
           
           <code><a href="plot_gene.html">plot_gene()</a></code> 
         </dt>
-        <dd>Plot function for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="plot_heatmap.html">plot_heatmap()</a></code> 
-        </dt>
-        <dd>Plotting function for class <code>'TAPACLOTH'</code>.</dd>
+        <dd>Plot function for class <code>'INCOMMON'</code>.</dd>
       </dl><dl><dt>
           
           <code><a href="plot_summary.html">plot_summary()</a></code> 
@@ -173,24 +107,14 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
         <dd>Plotting function for class <code>'TAPACLOTH'</code>.</dd>
       </dl><dl><dt>
           
-          <code><a href="plot_test.html">plot_test()</a></code> 
-        </dt>
-        <dd>Visualize classification results for individual observations.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="print.TAPACLOTH.html">print(<i>&lt;TAPACLOTH&gt;</i>)</a></code> 
-        </dt>
-        <dd>Print for class <code>'TAPACLOTH'</code>.</dd>
-      </dl><dl><dt>
-          
-          <code><a href="run_classifier.html">run_classifier()</a></code> 
+          <code><a href="posterior.html">posterior()</a></code> 
         </dt>
-        <dd>Classify mutations using a (Beta-)Binomial model-based test.</dd>
+        <dd>Getter for class <code>'INCOMMON'</code>.</dd>
       </dl><dl><dt>
           
-          <code><a href="test_setup.html">test_setup()</a></code> 
+          <code><a href="print.INCOMMON.html">print(<i>&lt;INCOMMON&gt;</i>)</a></code> 
         </dt>
-        <dd>Compute parameters and distribution for null hypothesis.</dd>
+        <dd>Print for class <code>'INCOMMON'</code>.</dd>
       </dl></div>
   </main></div>
 
@@ -200,7 +124,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 </div>
 
 <div class="pkgdown-footer-right">
-  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.6.</p>
+  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
 </div>
 
     </footer></div>
diff --git a/man/get_classifier.Rd b/man/classification.Rd
similarity index 64%
rename from man/get_classifier.Rd
rename to man/classification.Rd
index 24a328d..103714f 100644
--- a/man/get_classifier.Rd
+++ b/man/classification.Rd
@@ -1,13 +1,13 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/utils.R
-\name{get_classifier}
-\alias{get_classifier}
-\title{Getter for class \code{'TAPACLOTH'}.}
+\name{classification}
+\alias{classification}
+\title{Getter for class \code{'INCOMMON'}.}
 \usage{
-get_classifier(x, model = NULL)
+classification(x)
 }
 \arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
+\item{x}{An obj of class \code{'INCOMMON'}.}
 
 \item{model}{Model used in the test from which to get classification data.}
 }
diff --git a/man/classify.Rd b/man/classify.Rd
new file mode 100644
index 0000000..1ddd762
--- /dev/null
+++ b/man/classify.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/classify.R
+\name{classify}
+\alias{classify}
+\title{Classify mutations using a Beta-Binomial model-based test.}
+\usage{
+classify(
+  x,
+  priors = NULL,
+  entropy_cutoff = 0.2,
+  rho = 0.01,
+  karyotypes = c("1:0", "1:1", "2:0", "2:1", "2:2")
+)
+}
+\arguments{
+\item{x}{An object of class \code{'INCOMMON'} generated with function \code{init}.}
+
+\item{priors}{}
+
+\item{entropy_cutoff}{Entropy cut-off for Tier-1 vs Tier-2 assignment.}
+
+\item{rho}{Over-dispersion parameter.}
+
+\item{karyotypes}{Karyotypes to be included among the possible classes.}
+}
+\value{
+An object of class \code{INCOMMON} containing the original input plus
+the classification data and parameters.
+}
+\description{
+Classify mutations using a Beta-Binomial model-based test.
+}
+\examples{
+x = init(mutations = example_data$data,
+         sample = example_data$sample,
+         purity = example_data$purity,
+         tumor_type = example_data$tumor_type)
+x = classify(
+    x = x, 
+    priors = priors,
+    entropy_cutoff = 0.2,
+    rho = 0.01,
+    karyotypes = c("1:0","1:1","2:0","2:1","2:2")
+    )
+print(x)
+}
diff --git a/man/binomial_test.Rd b/man/compute_posterior.Rd
similarity index 66%
rename from man/binomial_test.Rd
rename to man/compute_posterior.Rd
index f511080..b462d17 100644
--- a/man/binomial_test.Rd
+++ b/man/compute_posterior.Rd
@@ -1,44 +1,52 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/binomial_test.R
-\name{binomial_test}
-\alias{binomial_test}
-\title{Compute likelihoods and uncertainty..}
+% Please edit documentation in R/compute_posterior.R
+\name{compute_posterior}
+\alias{compute_posterior}
+\title{Compute model likelihood, posterior and entropy}
 \usage{
-binomial_test(
-  test,
+compute_posterior(
+  NV,
   DP,
+  gene,
+  priors = NULL,
+  tumor_type,
   purity,
-  cutoff,
-  model,
+  entropy_cutoff,
   rho = 0.01,
   karyotypes,
   assign_extremes
 )
 }
 \arguments{
-\item{test}{Number of reads with the variant.}
+\item{NV}{Number of reads with the variant.}
 
 \item{DP}{Sequencing coverage of the mutated genome site.}
 
-\item{purity}{Purity of the sample.}
+\item{gene}{Gene name or symbol.}
 
-\item{cutoff}{Likelihood cut-off for class assignment.}
+\item{priors}{Prior distribution.}
 
-\item{model}{Model used for the classification task, either "Binomial" (no over-dispersion)
-or "Beta-Binomial" (over-dispersion included), that will be used as the expected
-distribution for the number of reads with variant at fixed coverage and purity.}
+\item{tumor_type}{Tumor type of the sample.}
+
+\item{purity}{Purity of the sample.}
+
+\item{entropy_cutoff}{Cut-off on entropy for Tier-1/Tier-2 distinction.}
 
 \item{rho}{If "Beta-Binomial" model is selected, this parameter tunes the over-dispersion
 of the expected distribution used for the classification.}
 
 \item{karyotypes}{Karyotypes to be included among the possible classes.}
+
+\item{model}{Model used for the classification task, either "Binomial" (no over-dispersion)
+or "Beta-Binomial" (over-dispersion included), that will be used as the expected
+distribution for the number of reads with variant at fixed coverage and purity.}
 }
 \value{
 A tibble including ploidy, multiplicity, proportion of wt alleles,
 uncertainty  of the class assignment, model density.
 }
 \description{
-Compute likelihoods and uncertainty..
+Compute model likelihood, posterior and entropy
 }
 \examples{
 binomial_test(test = 220,
diff --git a/man/estimate_purity.Rd b/man/estimate_purity.Rd
deleted file mode 100644
index f069d85..0000000
--- a/man/estimate_purity.Rd
+++ /dev/null
@@ -1,31 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/estimate_purity.R
-\name{estimate_purity}
-\alias{estimate_purity}
-\title{Infer sample purity using a mixture of Binomial or Beta-Binomial distributions.}
-\usage{
-estimate_purity(x, model = "Binomial", eps = 0.01)
-}
-\arguments{
-\item{x}{An object of class \code{'TAPACLOTH'} generated with function \code{init}.}
-
-\item{model}{The expected distribution for the number of reads with variant
-at fixed coverage and purity, that can be chosen between Binomial (no over-dispersion)
-or Beta-Binomial (over-dispersion included).}
-
-\item{eps}{In case data is fitted with a mixture of 2 distributions, sample purity
-is estimated using only that whose peak is closer to the input purity estimate
-than the value of this parameter. If both distributions satisfy this condition,
-the one which is closest to the input purity estimate is used for the new estimate.}
-}
-\value{
-An object of class \code{TAPACLOTH} containing the inferred purity.
-}
-\description{
-Infer sample purity using a mixture of Binomial or Beta-Binomial distributions.
-}
-\examples{
-input = init(mutations = example_data$data, sample = example_data$sample, purity = example_data$purity)
-out = estimate_purity(x = input, model = "binomial", eps = 0.01)
-print(out)
-}
diff --git a/man/gene_classification.Rd b/man/gene_classification.Rd
deleted file mode 100644
index 29345eb..0000000
--- a/man/gene_classification.Rd
+++ /dev/null
@@ -1,21 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{gene_classification}
-\alias{gene_classification}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-gene_classification(x, gene_id, model)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{gene_id}{The name of the gene.}
-
-\item{model}{Model used in the test from which to get classification data.}
-}
-\value{
-A tibble with gene-specific classification data.
-}
-\description{
-Get classification data for specific gene under the selected model.
-}
diff --git a/man/get_DP.Rd b/man/get_DP.Rd
deleted file mode 100644
index bc06d43..0000000
--- a/man/get_DP.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_DP}
-\alias{get_DP}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-get_DP(x, id)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{mutation_id}{Coordinates of mutation in the form of a string
-containing \code{chr},\code{from},\code{to},\code{alt},\code{ref} coordinates, colon separated.}
-}
-\value{
-DP of the mutation.
-}
-\description{
-Get coverage for a specific mutation in the sample.
-}
diff --git a/man/get_NV.Rd b/man/get_NV.Rd
deleted file mode 100644
index 302cee4..0000000
--- a/man/get_NV.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_NV}
-\alias{get_NV}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-get_NV(x, id)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{mutation_id}{Coordinates of mutation in the form of a string
-containing \code{chr},\code{from},\code{to},\code{alt},\code{ref} coordinates, colon separated.}
-}
-\value{
-NV of the mutation.
-}
-\description{
-Get number of reads with variant for a specific mutation in the sample.
-}
diff --git a/man/get_VAF.Rd b/man/get_VAF.Rd
deleted file mode 100644
index 2e483b1..0000000
--- a/man/get_VAF.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_VAF}
-\alias{get_VAF}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-get_VAF(x, mutation_id)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{mutation_id}{Coordinates of mutation in the form of a string
-containing \code{chr},\code{from},\code{to},\code{alt},\code{ref} coordinates, colon separated.}
-}
-\value{
-VAF of the mutation.
-}
-\description{
-Get variant allele frequency (VAF) for a specific mutation in the sample.
-}
diff --git a/man/get_classes.Rd b/man/get_classes.Rd
deleted file mode 100644
index c14fb3a..0000000
--- a/man/get_classes.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_classes}
-\alias{get_classes}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-get_classes(x, model)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{model}{Model used in the test from which to get classification data.}
-}
-\value{
-A tibble.
-}
-\description{
-Get significant classification data for the specified model, if already tested.
-}
diff --git a/man/get_coord.Rd b/man/get_coord.Rd
deleted file mode 100644
index 54a4a89..0000000
--- a/man/get_coord.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_coord}
-\alias{get_coord}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-get_coord(x, gene_name)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{gene_name}{Name of the gene affected by the mutation.}
-}
-\value{
-A list of mutation coordinates.
-}
-\description{
-Get coordinates of mutation(s) mapped on a specified gene.
-}
diff --git a/man/get_gene.Rd b/man/get_gene.Rd
deleted file mode 100644
index bfdd488..0000000
--- a/man/get_gene.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_gene}
-\alias{get_gene}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-get_gene(x, mutation_id)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{mutation_id}{Coordinates of mutation in the form of a string
-containing \code{chr},\code{from},\code{to},\code{alt},\code{ref} coordinates, colon separated.}
-}
-\value{
-A tibble with the name of the gene affected by the specified mutation.
-}
-\description{
-Get ID of the gene affected by the specified mutation.
-}
diff --git a/man/get_id.Rd b/man/get_id.Rd
deleted file mode 100644
index e5ba8cd..0000000
--- a/man/get_id.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_id}
-\alias{get_id}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-get_id(x, gene_name)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{gene_name}{Name of the selected gene.}
-}
-\value{
-ID( of mutation(s).
-}
-\description{
-Get ID of the mutation(s) affecting the specified gene
-}
diff --git a/man/get_purity_bmix.Rd b/man/get_purity_bmix.Rd
deleted file mode 100644
index e0d454a..0000000
--- a/man/get_purity_bmix.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_purity_bmix}
-\alias{get_purity_bmix}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-get_purity_bmix(x, model)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{model}{Model used for purity estimation}
-}
-\value{
-Sample purity as obtained by BMix purity estimation procedure.
-}
-\description{
-Extract the sample purity as estimated using the specified model
-}
diff --git a/man/get_purity_estimate.Rd b/man/get_purity_estimate.Rd
deleted file mode 100644
index f0041dd..0000000
--- a/man/get_purity_estimate.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_purity_estimate}
-\alias{get_purity_estimate}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-get_purity_estimate(x, model)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{model}{Model used for purity estimation}
-}
-\value{
-Purity estimate data.
-}
-\description{
-Extract data and parameters of purity estimation.
-}
diff --git a/man/get_reliability.Rd b/man/get_reliability.Rd
deleted file mode 100644
index 8945e9c..0000000
--- a/man/get_reliability.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{get_reliability}
-\alias{get_reliability}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-get_reliability(x, model)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{model}{Model used for purity estimation}
-}
-\value{
-Reliability of input purity estimate.
-}
-\description{
-Extract reliability of input sample purity as compared to TAPACLOTH estimate using the specified model.
-}
diff --git a/man/init.Rd b/man/init.Rd
index ca97c9e..45e1ee6 100644
--- a/man/init.Rd
+++ b/man/init.Rd
@@ -2,31 +2,39 @@
 % Please edit documentation in R/init.R
 \name{init}
 \alias{init}
-\title{Prepare input for analyses with \code{'TAPACLOTH'}.}
+\title{Prepare input for analyses with \code{'INCOMMON'}.}
 \usage{
-init(mutations, sample, purity, gene_roles = TAPACLOTH::cancer_gene_census)
+init(
+  mutations,
+  sample,
+  tumor_type,
+  purity,
+  gene_roles = INCOMMON::cancer_gene_census
+)
 }
 \arguments{
-\item{mutations}{a tibble with columns chromosome \code{chr}, start position \code{from}, end position \code{to},
-reference \code{ref} and alternative \code{alt} alleles, coverage \code{DP}, number
-of reads with variant \code{NV}, variant allelic frequency \code{VAF} gene name \code{gene}
+\item{mutations}{a tibble with columns mutant chromosome \code{chr}, mutation start position \code{from}, mutation end position \code{to},
+reference allel \code{ref}, alternative allele \code{alt}, integer sequencing depth \code{DP}, integer number
+of reads with variant \code{NV}, variant allelic frequency \code{VAF} and gene name \code{gene}
 as Hugo Symbol.}
 
-\item{sample}{Sample name.}
+\item{sample}{Sample name or ID.}
 
-\item{purity}{Sample purity.}
+\item{tumor_type}{Tumor type of the sample.}
 
-\item{gene_roles}{A tibble reporting a list of gene names \code{gene} and associated
-role \code{gene_role} among "oncogene", "TSG" and "fusion". Default is taken from COSMIC cancer gene census.}
+\item{purity}{Purity of the sample.}
+
+\item{gene_roles}{A tibble reporting a list of \code{gene} names and associated
+\code{gene_role} among "oncogene", "TSG" and "fusion". The default is taken from COSMIC Cancer Gene Census.}
 }
 \value{
-An object of class \code{TAPACLOTH}.
+An object of class \code{INCOMMON}.
 }
 \description{
-Process input data into an object of class \code{'TAPACLOTH'}, ready for
-analyses with \code{run_classifier} and \code{estimate_purity} functions.
+Process input data into an object of class \code{'INCOMMON'}, ready for
+dwonstream analyses (e.g. \code{classify_sample}).
 }
 \examples{
-input = init(mutations = example_data$data, sample = example_data$sample, purity = example_data$purity)
+input = init(mutations = example_data$data, sample = example_data$sample, purity = example_data$purity, tumor_type = example_data$tumor_type)
 print(input)
 }
diff --git a/man/models_avail.Rd b/man/models_avail.Rd
deleted file mode 100644
index 75480b1..0000000
--- a/man/models_avail.Rd
+++ /dev/null
@@ -1,17 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{models_avail}
-\alias{models_avail}
-\title{Getter for class \code{'TAPACLOTH'}.}
-\usage{
-models_avail(x)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-}
-\value{
-Model names.
-}
-\description{
-List models used for classification tests.
-}
diff --git a/man/get_params.Rd b/man/parameters.Rd
similarity index 64%
rename from man/get_params.Rd
rename to man/parameters.Rd
index 288affb..c2a0c37 100644
--- a/man/get_params.Rd
+++ b/man/parameters.Rd
@@ -1,13 +1,13 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/utils.R
-\name{get_params}
-\alias{get_params}
-\title{Getter for class \code{'TAPACLOTH'}.}
+\name{parameters}
+\alias{parameters}
+\title{Getter for class \code{'INCOMMON'}.}
 \usage{
-get_params(x, model)
+parameters(x)
 }
 \arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
+\item{x}{An obj of class \code{'INCOMMON'}.}
 }
 \value{
 A tibble containing parameters for all the models used in the classification.
diff --git a/man/plot.TAPACLOTH.Rd b/man/plot.INCOMMON.Rd
similarity index 74%
rename from man/plot.TAPACLOTH.Rd
rename to man/plot.INCOMMON.Rd
index bdaebf7..7310b0c 100644
--- a/man/plot.TAPACLOTH.Rd
+++ b/man/plot.INCOMMON.Rd
@@ -1,13 +1,13 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/print.tapacloth.R
-\name{plot.TAPACLOTH}
-\alias{plot.TAPACLOTH}
-\title{Plot for class \code{'TAPACLOTH'}.}
+% Please edit documentation in R/print.INCOMMON.R
+\name{plot.INCOMMON}
+\alias{plot.INCOMMON}
+\title{Plot for class \code{'INCOMMON'}.}
 \usage{
-plot.TAPACLOTH(x, ...)
+\method{plot}{INCOMMON}(x, ...)
 }
 \arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
+\item{x}{An obj of class \code{'INCOMMON'}.}
 
 \item{...}{Default S3 method parameter.}
 }
@@ -24,5 +24,5 @@ a plot showing details of the used statistical test in the bottom panel.
 input = init(mutations = example_data$data[1,], sample = example_data$sample, purity = example_data$purity)
 x = run_classifier(input, alpha_level = 1e-3, model = "Binomial")
 x = plot_test(x)
-plot.TAPACLOTH(x)
+plot.INCOMMON(x)
 }
diff --git a/man/plot_bmix.Rd b/man/plot_bmix.Rd
deleted file mode 100644
index 841d506..0000000
--- a/man/plot_bmix.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{plot_bmix}
-\alias{plot_bmix}
-\title{Plot function for class \code{'TAPACLOTH'}.}
-\usage{
-plot_bmix(x, model)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{model}{Model used for purity estimate}
-}
-\value{
-A plot of BMix fit.
-}
-\description{
-Plot results of the BMix fit used for purity estimation, under the specified model.
-}
diff --git a/man/plot_classification.Rd b/man/plot_classification.Rd
new file mode 100644
index 0000000..9cfe1d4
--- /dev/null
+++ b/man/plot_classification.Rd
@@ -0,0 +1,32 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/plot_classification.R
+\name{plot_classification}
+\alias{plot_classification}
+\title{Visualize classification results for individual observations.}
+\usage{
+plot_classification(x, assembly = F)
+}
+\arguments{
+\item{x}{An object of class \code{'INCOMMON'} containing the classification results, as
+produced by function \code{classify}.}
+}
+\value{
+An object or a list of objects of class \code{'ggplot2'}.
+}
+\description{
+Visualize classification results for individual observations.
+}
+\examples{
+x = init(mutations = example_data$data,
+         sample = example_data$sample,
+         purity = example_data$purity,
+         tumor_type = example_data$tumor_type)
+x = classify(
+    x = x, 
+    priors = priors,
+    entropy_cutoff = 0.2,
+    rho = 0.01,
+    karyotypes = c("1:0","1:1","2:0","2:1","2:2")
+    )
+plot_test(x = x, id = ids(x)[1])
+}
diff --git a/man/plot_gene.Rd b/man/plot_gene.Rd
index 154663e..6d17a30 100644
--- a/man/plot_gene.Rd
+++ b/man/plot_gene.Rd
@@ -2,12 +2,12 @@
 % Please edit documentation in R/utils.R
 \name{plot_gene}
 \alias{plot_gene}
-\title{Plot function for class \code{'TAPACLOTH'}.}
+\title{Plot function for class \code{'INCOMMON'}.}
 \usage{
 plot_gene(x, model, gene_name)
 }
 \arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
+\item{x}{An obj of class \code{'INCOMMON'}.}
 
 \item{model}{Model used for classification.}
 
diff --git a/man/plot_heatmap.Rd b/man/plot_heatmap.Rd
deleted file mode 100644
index df75ef0..0000000
--- a/man/plot_heatmap.Rd
+++ /dev/null
@@ -1,25 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_heatmap.R
-\name{plot_heatmap}
-\alias{plot_heatmap}
-\title{Plotting function for class \code{'TAPACLOTH'}.}
-\usage{
-plot_heatmap(x, model = "binomial")
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'} containing a \code{classifier}.}
-
-\item{model}{Model used for the test, either "Binomial" or "Beta-Binomial".}
-}
-\value{
-An object of class \code{'TAPACLOTH'} containing a list of ggplot2
-plots named \code{plot_test} inside \code{classifier}.
-}
-\description{
-Generates a composite heatmap with useful information on data and classification results.
-}
-\examples{
-x = init(mutations = example_data$data, sample = example_data$sample, purity = example_data$purity)
-x = run_classifier(x)
-plot_heatmap(x)
-}
diff --git a/man/plot_summary.Rd b/man/plot_summary.Rd
index 3fb4bab..426e155 100644
--- a/man/plot_summary.Rd
+++ b/man/plot_summary.Rd
@@ -4,7 +4,13 @@
 \alias{plot_summary}
 \title{Plotting function for class \code{'TAPACLOTH'}.}
 \usage{
-plot_summary(x, model = "binomial")
+plot_summary(
+  x,
+  model = "binomial",
+  out_file = "./tapacloth_pheatmap.pdf",
+  main = "summary statistics of classification",
+  n_frequency_colors = 4
+)
 }
 \arguments{
 \item{x}{A list of obj of class \code{'TAPACLOTH'} containing a \code{classifier}.}
diff --git a/man/plot_test.Rd b/man/plot_test.Rd
deleted file mode 100644
index 1371879..0000000
--- a/man/plot_test.Rd
+++ /dev/null
@@ -1,33 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/plot_test.R
-\name{plot_test}
-\alias{plot_test}
-\title{Visualize classification results for individual observations.}
-\usage{
-plot_test(x, model, assembly = F)
-}
-\arguments{
-\item{x}{An object of class \code{'TAPACLOTH'} containing the classification results, as
-produced by function \code{run_classifier}.}
-
-\item{model}{Model used for the classification task.}
-}
-\value{
-An object of class \code{'ggplot2'}.
-}
-\description{
-Visualize classification results for individual observations.
-}
-\examples{
-x = init(mutations = example_data$data,
-         sample = example_data$sample,
-         purity = example_data$purity)
-model = "beta-binomial"
-x = run_classifier(
-    x = x, 
-    model = model, 
-    rho = 0.01,
-    karyotypes = c("1:0","1:1","2:0","2:1","2:2")
-    )
-plot_test(x = x,id = x$classifier[[model]]data$id[1],model = model)
-}
diff --git a/man/posterior.Rd b/man/posterior.Rd
new file mode 100644
index 0000000..90a3ddf
--- /dev/null
+++ b/man/posterior.Rd
@@ -0,0 +1,17 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{posterior}
+\alias{posterior}
+\title{Getter for class \code{'INCOMMON'}.}
+\usage{
+posterior(x, id)
+}
+\arguments{
+\item{x}{An obj of class \code{'INCOMMON'}.}
+}
+\value{
+A tibble containing parameters for all the models used in the classification.
+}
+\description{
+Get model parameters of the performed classification tests.
+}
diff --git a/man/print.INCOMMON.Rd b/man/print.INCOMMON.Rd
new file mode 100644
index 0000000..fd5384f
--- /dev/null
+++ b/man/print.INCOMMON.Rd
@@ -0,0 +1,33 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/print.INCOMMON.R
+\name{print.INCOMMON}
+\alias{print.INCOMMON}
+\title{Print for class \code{'INCOMMON'}.}
+\usage{
+\method{print}{INCOMMON}(x, ...)
+}
+\arguments{
+\item{x}{An obj of class \code{'INCOMMON'}.}
+
+\item{...}{Default S3 method parameter.}
+}
+\value{
+Nothing.
+}
+\description{
+Print for class \code{'INCOMMON'}.
+}
+\examples{
+x = init(mutations = example_data$data,
+         sample = example_data$sample,
+         purity = example_data$purity,
+         tumor_type = example_data$tumor_type)
+x = classify(
+    x = x, 
+    priors = priors,
+    entropy_cutoff = 0.2,
+    rho = 0.01,
+    karyotypes = c("1:0","1:1","2:0","2:1","2:2")
+    )
+print(x)
+}
diff --git a/man/print.TAPACLOTH.Rd b/man/print.TAPACLOTH.Rd
deleted file mode 100644
index 706a9b9..0000000
--- a/man/print.TAPACLOTH.Rd
+++ /dev/null
@@ -1,30 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/print.tapacloth.R
-\name{print.TAPACLOTH}
-\alias{print.TAPACLOTH}
-\title{Print for class \code{'TAPACLOTH'}.}
-\usage{
-\method{print}{TAPACLOTH}(x, ...)
-}
-\arguments{
-\item{x}{An obj of class \code{'TAPACLOTH'}.}
-
-\item{...}{Default S3 method parameter.}
-}
-\value{
-Nothing.
-}
-\description{
-Print for class \code{'TAPACLOTH'}.
-}
-\examples{
-x = init(mutations = example_data$data,
-         sample = example_data$sample,
-         purity = example_data$purity)
-x = run_classifier(
-    x, 
-    alpha_level = 1e-3, 
-   model = "Binomial")
-x = estimate_purity(x = x, model = "binomial", eps = 0.01)
-print(x)
-}
diff --git a/man/run_classifier.Rd b/man/run_classifier.Rd
deleted file mode 100644
index 7c4d295..0000000
--- a/man/run_classifier.Rd
+++ /dev/null
@@ -1,49 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/run_classifier.R
-\name{run_classifier}
-\alias{run_classifier}
-\title{Classify mutations using a (Beta-)Binomial model-based test.}
-\usage{
-run_classifier(
-  x,
-  cutoff = 0.75,
-  model = "Binomial",
-  rho = 0.01,
-  karyotypes = c("1:0", "1:1", "2:0", "2:1", "2:2"),
-  gene_role_specific = FALSE,
-  assign_extremes = FALSE
-)
-}
-\arguments{
-\item{x}{An object of class \code{'TAPACLOTH'} generated with function \code{init}.}
-
-\item{cutoff}{Likelihood cut-off for class assignment.}
-
-\item{model}{Model used for the classification task, either "Binomial" (no over-dispersion)
-or "Beta-Binomial" (over-dispersion included), that will be used as the expected
-distribution for the number of reads with variant at fixed coverage and purity.}
-
-\item{rho}{If "Beta-Binomial" model is selected, this parameter tunes the over-dispersion
-of the expected distribution used for the test.}
-
-\item{karyotypes}{Karyotypes to be included among the possible classes.}
-}
-\value{
-An object of class \code{TAPACLOTH} containing the input plus
-the classification data and paramters.
-}
-\description{
-Classify mutations using a (Beta-)Binomial model-based test.
-}
-\examples{
-x = init(mutations = example_data$data,
-         sample = example_data$sample,
-         purity = example_data$purity)
-x = run_classifier(
-    x = x, 
-    model = "Beta-Binomial", 
-    rho = 0.01,
-    karyotypes = c("1:0","1:1","2:0","2:1","2:2")
-    )
-print(x)
-}
diff --git a/man/test_setup.Rd b/man/test_setup.Rd
deleted file mode 100644
index f20e169..0000000
--- a/man/test_setup.Rd
+++ /dev/null
@@ -1,36 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/test_setup.R
-\name{test_setup}
-\alias{test_setup}
-\title{Compute parameters and distribution for null hypothesis.}
-\usage{
-test_setup(
-  coverage = 500,
-  purity = 1,
-  rho = 0.01,
-  threshold = 0.1,
-  model = "binomial",
-  karyotypes = c("1:0", "1:1", "2:0", "2:1", "2:2")
-)
-}
-\arguments{
-\item{coverage}{The sequencing coverage at the locus of mutation.}
-
-\item{purity}{Sample purity.}
-
-\item{rho}{The overdisperion parameter for "Beta-Binomial" model.}
-
-\item{model}{Model used for the test, either "Binomial" or "Beta-Binomial".}
-
-\item{alpha_level}{The confidence level of the test.}
-}
-\value{
-A list.
-}
-\description{
-Compute parameters and distribution for null hypothesis.
-}
-\examples{
-null_model = test_setup(coverage = 500, purity = 1.0, rho = 0.01, alpha_level = 0.01, model = 'binomial') 
-print(null_model)
-}
diff --git a/vignettes/classify-and-plot.Rmd b/vignettes/Classify_Mutations.Rmd
similarity index 54%
rename from vignettes/classify-and-plot.Rmd
rename to vignettes/Classify_Mutations.Rmd
index 338881d..2347551 100644
--- a/vignettes/classify-and-plot.Rmd
+++ b/vignettes/Classify_Mutations.Rmd
@@ -1,8 +1,8 @@
 ---
-title: "Classify karyotype and multiplicity"
+title: "Classify mutations from a targeted sequencing sample"
 output: rmarkdown::html_vignette
 vignette: >
-  %\VignetteIndexEntry{Classify clonality and zygosity}
+  %\VignetteIndexEntry{Classify mutations from a targeted sequencing sample}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -18,10 +18,10 @@ options(crayon.enabled=TRUE)
 
 ```{r setup}
 library(dplyr)
-library(TAPACLOTH)
+library(INCOMMON)
 ```
 
-We work with the [example TAPACLOTH `data`](TAPACLOTH.html).
+We work with the [example INCOMMON `data`](INCOMMON.html).
 
 ```{r, include=FALSE}
 print(example_data)
@@ -64,49 +64,50 @@ The input must be prepared using function `init`:
 input = init(mutations = example_data$data,
              sample = example_data$sample,
              purity = example_data$purity,
+             tumor_type = example_data$tumor_type,
              gene_roles = cancer_gene_census)
 print(input)
 ```
-A column `gene_role` is attached to the input data, indicating the function of the
-affected gene as described in COSMIC Cancer Gene Census (default). Other descriptions can
-be input by the user through option `gene_role` of function `init`.
-
-A cut-off $\alpha$ on the likelihood can be used in the classification in order to
-discard classifications with poor likelihoods.
-For each run of `run_classifier` using a certain model, a `classifier` object is 
-attached to the input, containing the model parameters (cut-off, overdispersion) and 
-the outcome of the classifier, including a measure of classification uncertainty.
-By default, ploidies corresponding to karyotypes 1:0, 1:1, 2:0, 2:1 and 2:2 are 
-tested. Other karyotypes can be provided by the user through option `karyotypes`.
+A column `gene_role` is extracted from the COSMIC Cancer Gene Census (default) catalogue and 
+attached to the input data according to gene names. Other sources for gene roles can
+be input by the user through option `gene_roles` of function `init`.
+
+INCOMMON classification of a sample can be performed using function `classify`. 
 
 ```{r}
-out = run_classifier(
+out = classify(
   x = input,
-  cutoff = 0.75,
-  model = "Binomial"
+  priors = pcawg_priors,
+  entropy_cutoff = NULL,
+  rho = 0.01
 )
-
-out = run_classifier(
-    x = out,
-    cutoff = 0.75,
-    model = "Beta-Binomial",
-    rho = 0.01
-    )
-
 print(out)
 ```
 The results of the classification task can be visualized using the internal 
-plotting function. Here is an example using the Binomial model:
+plotting function. Here is an example:
 ```{r}
-plots = plot_test(out, model = "binomial")
-plots[[1]]
+plot_classification(out)
 ```
-And the Beta-Binomial model:
+All mutations are classified as with amplification. However visual inspection of the plots
+suggest that some of the mutations are hard to classify because of uncertainty. The number of
+reads with the variant $NV$ (vertical line) in these cases is compatible with multiple copy number
+configurations, which are assigned similar posterior probabilities.
+
+One can make the classification stricter by using the entropy cut-off in function `classify`.
+Mutations with classification entropy above this cutoff will be flagged as Tier-2.
+The default entropy cutoff is 0.20.
+
 ```{r}
-plots = plot_test(out, model = "beta-binomial")
-plots[[1]]
+out = classify(
+  x = input,
+  priors = pcawg_priors,
+  entropy_cutoff = 0.2,
+  rho = 0.01
+)
+print(out)
 ```
 
-This example shows differences in the classification task in terms of expected distributions 
-under the Binomial and the Beta-Binomial models. In this case the assigned class is the same,
-but the classification uncertainty is shown to be larger for the Beta-Binomial case.
+In this scenario, all mutations are flagged as Tier-2, except KRAS that is classified as an amplified mutation (AM).
+```{r}
+plot_classification(out)
+```
\ No newline at end of file
diff --git a/vignettes/INCOMMON.Rmd b/vignettes/INCOMMON.Rmd
new file mode 100644
index 0000000..f7e672a
--- /dev/null
+++ b/vignettes/INCOMMON.Rmd
@@ -0,0 +1,71 @@
+---
+title: "INCOMMON"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{INCOMMON}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+
+options(crayon.enabled=F)
+```
+
+
+INCOMMON is a tool for the INference of COpy number and Mutation Multiplicity in ONcology.
+INCOMMON infers the copy number and multiplicity of somatic mutations from tumour-only read count data, 
+and can be applied to classify mutations from large-size datasets in an efficient and fast way. 
+Mutations are classified as either Tier-1 (present in 100% cells) without copy-number alterations 
+(heterozygous mutant diploid HMD), with loss of heterozygosity (LOH), copy-neutral LOH (CNLOH),
+amplification (AM), or Tier-2 (subclonal or with high ploidy and low multiplicity).
+
+> The INCOMMON model is designed to work with high-resolution targeted data such as 
+targeted panels but, in principle, it can be used with any sequencing assay. INCOMMON
+is helpful also to analyse sequencing data from tumor-only assays, in paricular when alignment
+files (fastq, bam, etc.) are not availble.
+However, if one can access  higher-resolution whole-exome or whole-genome assays, specific [deconvolution methodologies should be used](https://caravagnalab.github.io/mobster, https://github.com/caravagnalab/CNAqc). 
+
+## Copy number and mutation multiplicity assessment
+
+INCOMMON will assess, for every mutation, any of the following statuses:
+
+- Ploidy among 
+  - 1 (loss of heterozygosity LOH), 
+  - 2 (heterozygous and homozygous),
+  - 3 (trisomy), 
+  - 4 (tetrasomy);
+- Multiplicity between 1 and 2;
+
+INCOMMON implements [a classifier based on maximum a posteriori estimation](Classify_Mutations.html); the required inputs are:
+
+- read counts of a mutation
+- purity of the tumour sample $\pi > 0$
+
+> Tumour sample purity $\pi$ can be estimated by copy number assessment, pathology assessment, or  in general any other bioinformatics approach outside INCOMMON. INCOMMON assumes that the input purity is correct.
+
+##  Input format
+
+Input must be prepared using the function `init`. The input to this function must contain:
+
+- `mutations`: a tibble or dataframe containing the mutations in a sample. Columns should indicate coordinates (chromosome `chr`, start position `from`,
+end position `to`), type of substitution (reference `ref` and alternative `alt` alleles), sequencing coverage `DP`, number
+of reads with the variant `NV`, variant allelic frequency `VAF` and gene name `gene` (preferably as Hugo Symbol)
+- `sample`:  name or ID of the sample
+- `purity`, tumor sample purity
+
+This is an example input dataset.
+
+```{r, include=FALSE}
+x = init(
+  mutations = example_data$data,
+  sample = example_data$sample,
+  purity = example_data$purity,
+  tumor_type = example_data$tumor_type
+)
+print.INCOMMON(x)
+```
diff --git a/vignettes/TAPACLOTH.Rmd b/vignettes/TAPACLOTH.Rmd
deleted file mode 100644
index 213548c..0000000
--- a/vignettes/TAPACLOTH.Rmd
+++ /dev/null
@@ -1,73 +0,0 @@
----
-title: "TAPACLOTH"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{TAPACLOTH}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-```{r, include = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
-
-options(crayon.enabled=F)
-```
-
-
-TAPACLOTH is a package to process targeted panel sequencing data of a tumour-matched normal cancer sample and perform clonal deconvolution. The tool allows to:
-
-- classify the ploidy and multiplicity of somatic mutations detected by the panel;
-- asses tumour purity from somatic mutations detected by the panel;
-
-> The TAPACLOTH model is designed to work with a target panel but, in principle, it can be used with any sequencing assay. However, if one can access  higher-resolution whole-exome or whole-genome assays, specific [deconvolution methodologies should be used](https://caravagnalab.github.io/mobster). 
-
-## Ploidy and multiplicity assessment
-
-TAPACLOTH will assess, for every mutation, any of the following statuses:
-
-- ploidy among 
-  - 1 (LOH), 
-  - 2 (diploid heterozygous and copy-neutral LOH), , 
-  - 3 (trisomy), 
-  - 4 (tetrasomy);
-- multiplicity between 1 and 2 for ploidy greater than 1;
-
-TAPACLOTH implements [a classifier based on maximum likelihood estimation](classify-and-plot.html); the required inputs are:
-
-- read/counts from the panel assay 
-- tumour sample purity $\pi > 0$
-
-> Tumour sample purity $\pi$ can be estimated by copy number assessment, pathology assessment, or  in general any other bioinformatics approach outside TAPACLOTH.
-
-For classification, TAPACLOTH assumes that the input purity is correct, an assert that can be tested by estimating purity from TAPACLOTH directly.
-
-## Purity assessment
-
-TAPACLOTH can be used to [estimate the purity of the cancer sample](purity-estimates.html) from the spectrum of somatic mutations detected from targeted panel sequencing; the required inputs are:
-
-- read/counts or variant allele frequencies from the panel assay.
-
-If an estimate of tumour sample purity, made for example by copy number  or pathology assessment, is provided as input, TAPACLOTH additionally computes  a reliability score for the estimate.
-
-##  Inputs format
-
-For all tests, input must be prepared using function `init`, providing as input
-the following data:
-
-- `mutations` as a tibble with columns indicating chromosome `chr`, start position `from`,
-end position `to`, reference `ref` and alternative `alt` alleles, coverage `DP`, number
-of reads with variant `NV`, variant allelic frequency `VAF` and gene name `gene` as Hugo Symbol;
-- `sample`, for name of the sample;
-- `purity`, for sample purity;
-
-This is an example input dataset.
-
-```{r, include=FALSE}
-x = TAPACLOTH::init(mutations = TAPACLOTH::example_data$data,
-                    sample = TAPACLOTH::example_data$sample,
-                    purity = TAPACLOTH::example_data$purity)
-TAPACLOTH:::print.TAPACLOTH(x)
-```
diff --git a/vignettes/purity-estimates.Rmd b/vignettes/purity-estimates.Rmd
deleted file mode 100644
index 5767df3..0000000
--- a/vignettes/purity-estimates.Rmd
+++ /dev/null
@@ -1,165 +0,0 @@
----
-title: "Purity estimates"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{Purity estimates}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-```{r, include = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
-
-options(crayon.enabled=TRUE)
-```
-
-```{r setup}
-library(dplyr)
-library(TAPACLOTH)
-```
-
-
-We work with the [example TAPACLOTH `data`](TAPACLOTH.html).
-
-```{r, include=FALSE}
-print(example_data)
-```
-
-
-# Mixture-model based purity estimate
-
-TAPACLOTH infers sample purity by fitting the number of reads with variant of somatic mutations
-with a mixture of Binomial or Beta-Binomial distributions, using 
-[BMix](https://caravagnalab.github.io/BMix). 
-
-The BMix fit is performed using Binomial or Beta-Binomial mixture models with 1 up to 3
-clusters, and the best model is selected. Purity is estimated as twice the 
-mean of the mixture component that is expected to represent the cluster
-of clonal heterozygous mutations. The selected component is the one with lowest
-mean if data are fitted with two components, with intermediate mean if data are
-fitted with three components. 
-
-In case data are fit with a mixture of two components,
-we do not have any expectation on which one represents the clonal heterozygous cluster.
-In this case we adopt a conservative strategy and select the component that results 
-in the closest estimate to the input purity, if available, given that they are not
-more distant than the input parameter `eps`.
-
-## Example
-
-In this example, the input purity estimate of the cancer sample is correct, and 
-the VAF spectrum of somatic mutations is fit using a mixture of Binomial distributions.
-
-The input must be prepared using function `init`:
-```{r}
-input = init(mutations = example_data$data,
-             sample = example_data$sample,
-             purity = example_data$purity)
-print(input)
-```
-
-```{r}
-out = estimate_purity(input,
-                model = "Beta-Binomial",
-                eps = 0.01)
-
-print(out)
-```
-
-This test shows that the inferred purity matches the true value with a reliability
-score of 100%.
-
-If we provide an input purity of the cancer sample that is underestimated
-with respect to ground-truth, TAPACLOTH retrieves the correct purity value
-and reports the corresponding reliability score for the input estimate.
-
-```{r}
-# Example error with purity = 0.4
-input = init(mutations = example_data$data,
-             sample = example_data$sample,
-             purity = 0.7) # wrong purity!
-
-
-out = estimate_purity(
-  input,
-  model = "binomial",
-  eps = 0.01)
-
-print(out)
-```
-In this example TAPACLOTH estimates the correct purity (0.91) and assign a reliability
-of 0.77 to the input (under-estimated) purity. 
-
-Results of the fitting procedure are shown in a plot in `out$purity_estimate$binomial$plot_bmix`.
-
-The output plot shows (left) the assignment of variants to the fitted mixture components, 
-(center) the fitted densities and a comparison between the tested model, based on three
-different likelihood measures (BIC, ICL and NLL).
-
-```{r fig.height=4, fig.width=8, dpi=300}
-plot_bmix(out, model = "Binomial")
-```
-
-# Classifier re-run with the inferred purity
-
-TAPACLOTH purity estimate can be used as a preliminary step to the [classification task](classify-and-plot.html), especially when the input estimate is not 
-available or is considered unreliable.
-
-## Example
-
-In this example, the classification task is first run with an underestimated 
-input purity. 
-
-```{r}
-input = init(mutations = example_data$data,
-             sample = example_data$sample,
-             purity = 0.7) # wrong purity!
-
-classified_wrong = run_classifier(
-  input,
-  cutoff = 0.75,
-  model = "Beta-Binomial",
-  rho = 0.01
-)
-
-plt_wrong = plot_test(x = classified_wrong, model = "beta-binomial")[[1]]
-```
-
-In the following example the value of purity is replaced with the TAPACLOTH estimate 
-and the classification task is re-run with the new value.
-
-```{r}
-input = estimate_purity(
-  input,
-  model = "Beta-Binomial",
-  eps = 0.01)
-
-input$purity = get_purity_bmix(input, model = "beta-binomial")
-
-classified_right = run_classifier(
-  input,
-  cutoff = 0.75,
-  model = "Beta-Binomial",
-  rho = 0.01
-)
-
-plt_right = plot_test(classified_right, model = "beta-binomial")[[1]]
-```
-
-The two classifications can now be compared.
-
-```{r fig.height=6, fig.width=8, dpi=300}
-ggpubr::ggarrange(plotlist = list(
-  plt_wrong,
-  plt_right
-  ),
-ncol = 1,
-nrow = 2)
-```
-This example shows the impact of an incorrect purity estimate on the classification
-of variants, and how TAPACLOTH can be used to improve the results when the input
-estimate is not reliable enough. An incorrect purity estimate can result in a bad
-variant classification and this can eventually lead to wrong conclusions in downstream analyses.