fixed issue with copy number correction

There was an issue with the use of the cellular prevalence in the copy number correction post-processing step. The issue is now fixed and cellular prevalence is properly used in the computation of the new corrected copy number.
gavinha · Oct 23, 2018 · eb288ea · eb288ea
1 parent b39a30d
commit eb288ea
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/R/utils.R b/R/utils.R
@@ -1223,8 +1223,8 @@ correctIntegerCN <- function(cn, segs, purity, ploidy, maxCNtoCorrect.autosomes
 }
 
 ## compute copy number using corrected log ratio ##
-logRbasedCN <- function(x, purity, ploidyT, cellPrev, cn = 2){
-	if (is.null(cellPrev) || is.na(cellPrev)){
+logRbasedCN <- function(x, purity, ploidyT, cellPrev=NA, cn = 2){
+	if (length(cellPrev) == 1 && is.na(cellPrev)){
 		cellPrev <- 1
 	}
 	ct <- (2^x