fix cell composition cluster and pca components higher than sample size

umr1283 · May 3, 2019 · ae03004 · ae03004
1 parent 0c7b68a
commit ae03004
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Showing 11 changed files with 8 additions and 7 deletions.
diff --git a/CARoT.Rproj b/CARoT.Rproj
diff --git a/DESCRIPTION b/DESCRIPTION
diff --git a/LICENSE b/LICENSE
diff --git a/NAMESPACE b/NAMESPACE
diff --git a/NEWS.md b/NEWS.md
diff --git a/R/qc_idats.Rmd b/R/qc_idats.Rmd
@@ -380,7 +380,7 @@ ggplot2::ggplot(
     linetype = 2,
     na.rm = TRUE
   ) +
-  ggplot2::labs(x = "CpGs", y = "Call Rate", caption = "Only CPGs with a call aate stricly below 100 % are shown") +
+  ggplot2::labs(x = "CpGs", y = "Call Rate", caption = "Only CpGs with a call rate strictly below 100 % are shown") +
   ggplot2::scale_y_continuous(label = scales::percent) +
 	ggplot2::scale_x_continuous(label = scales::comma)
 ```
@@ -431,7 +431,7 @@ cell_comp <- switch(
     cat("No method defined yet")
   },
   {
-    estimate_k_cluster <- function(Rmat, max_k = 10, n_cores = 1) {
+    estimate_k_cluster <- function(Rmat, max_k = 25, n_cores = 1) {
       svdRmat <- RefFreeEWAS::svdSafe(Rmat)
       tmp <- do.call("rbind", parallel::mclapply(
         X = 0:max_k,
@@ -470,10 +470,11 @@ cell_comp <- switch(
       )
     }
     beta_matrix <- minfi::getBeta(data_mset)
+    max_k <- min(ncol(beta_matrix), 25)
     k_estimated <- min(estimate_k_cluster(
       Rmat = beta_matrix, 
-      max_k = 25, 
-      n_cores = min(params[["n_cores"]], 25)
+      max_k = max_k, 
+      n_cores = min(params[["n_cores"]], max_k)
     )$best)
     mu0 <- RefFreeEWAS::RefFreeCellMixInitialize(
       Y = minfi::getBeta(data_mset),
@@ -712,7 +713,7 @@ data_mset@metadata <- list(cnbeta = norm_beta)
 ```
 
 ```{r export}
-readr::write_rds(x = data_mset, path = paste0(output_directory, "/", script_name, "_mset.rds"))
+readr::write_rds(x = data_mset, path = paste0(output_directory, "/", params[["array"]], "_mset.rds"))
 ```
 
 ```{r pca}
@@ -734,8 +735,8 @@ for (ibeta in seq_along(list_beta)) {
 		design = minfi::pData(data_mset), 
 		id_var = "Sample_ID",
 		technical_vars = pca_vars, 
-		n_comp = 10, 
-		fig_n_comp = 3,
+		n_comp = min(10, ncol(data_batch[[names(list_beta)[ibeta]]])), 
+		fig_n_comp = min(3, ncol(data_batch[[names(list_beta)[ibeta]]])),
 		title_level = 4
 	)
 	cat("\n")

diff --git a/README.Rmd b/README.Rmd
diff --git a/README.md b/README.md
diff --git a/_pkgdown.yml b/_pkgdown.yml
diff --git a/appveyor.yml b/appveyor.yml
diff --git a/codecov.yml b/codecov.yml