cleaning up code

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", , "[email protected]", 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)

LICENSE

@@ -1,2 +1,2 @@
 YEAR: 2022
-COPYRIGHT HOLDER: TAPACLOTH authors
+COPYRIGHT HOLDER: INCOMMON authors

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)