Version 1.0.5: updated EPIC to remove genes from bulk that have only …

…NA values.
GfellerLab · Aug 28, 2017 · 6df4f24 · 6df4f24
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: EPIC
 Type: Package
 Title: Estimate the Proportion of Immune and Cancer cells
-Version: 1.0.4
+Version: 1.0.5
 Authors@R: as.person(c(
   "Julien Racle <[email protected]> [aut, cre]",
   "David Gfeller <[email protected]> [aut]"

diff --git a/NEWS b/NEWS
@@ -1,3 +1,7 @@
+Version 1.0.5
+------------------------------------------------------------------------
+* Updated EPIC to remove genes from bulk that have only NA values.
+
 Version 1.0.4
 ------------------------------------------------------------------------
 * Changed the name "scaleRefProf" to "scaleExprs" and made this boolean makes

diff --git a/R/EPIC_fun.R b/R/EPIC_fun.R
@@ -170,6 +170,11 @@ EPIC <- function(bulk, reference=NULL, mRNA_cell=NULL, mRNA_cell_sub=NULL,
 
   # Keeping only common genes and normalizing the counts based on these common
   # genes
+  bulk_NA <- apply(is.na(bulk), MARGIN=1, FUN=all)
+  if (any(bulk_NA)){
+    warning(sum(bulk_NA), " genes are NA in all bulk samples, removing these.")
+    bulk <- bulk[!bulk_NA,]
+  }
   bulkGenes <- rownames(bulk)
   if (anyDuplicated(bulkGenes))
     stop("There are some duplicated gene names in 'bulk'")