added a flag for the new addition to findDiploidLogR

veseshan · veseshan · commit 4b3c7acf7fad · 2016-01-11T17:12:13.000-05:00
diff --git a/R/facets-findDipLogR.R b/R/facets-findDipLogR.R
@@ -113,6 +113,7 @@ findDiploidLogR <- function(out, cnlr) {
         # cflor > cflr+0.1 because mafR can be low with 1+0 & 2+0 mixture
         if (sum(out1$num.mark[cflor > cflr+0.1])/nsnps > 0.05) {
             not1plus1 <- TRUE
+            flags <- c(flags, paste("mafR larger than expected if", dipLogR[1], "is diploid level"))
         }
         # assume dipLogR[1] is clonal 2+2 get acn consistent with cnlr, mafR
         # search acn from 3+0, 2+0 & 1+0; as 2+1 looks like 2+0 with lower cf

Original file line number	Diff line number	Diff line change
`@@ -113,6 +113,7 @@ findDiploidLogR <- function(out, cnlr) {`
`113`	`113`	`# cflor > cflr+0.1 because mafR can be low with 1+0 & 2+0 mixture`
`114`	`114`	`if (sum(out1$num.mark[cflor > cflr+0.1])/nsnps > 0.05) {`
`115`	`115`	`not1plus1 <- TRUE`
	`116`	`+ flags <- c(flags, paste("mafR larger than expected if", dipLogR[1], "is diploid level"))`
`116`	`117`	`}`
`117`	`118`	`# assume dipLogR[1] is clonal 2+2 get acn consistent with cnlr, mafR`
`118`	`119`	`# search acn from 3+0, 2+0 & 1+0; as 2+1 looks like 2+0 with lower cf`