Merge branch 'master' of https://github.com/steverozen/ICAMS

steverozen · Jul 18, 2019 · 4cd31ad · 4cd31ad
2 parents 46fdc5a + e23a3c2
commit 4cd31ad
Showing 1 changed file with 4 additions and 4 deletions.
diff --git a/R/VCF_to_catalog_functions.R b/R/VCF_to_catalog_functions.R
@@ -243,7 +243,7 @@ ReadMutectVCF <- function(file) {
 #'
 #' @export
 GetMutectVAF <-function(vcf) {
-  stopifnot(class(vcf) == "data.frame")
+  stopifnot("data.frame" %in% class(vcf))
   if (!any(grepl("/1", unlist(vcf[1, ])))) {
     stop("vcf does not appear to be a Mutect VCF, please check the data")
   }
@@ -269,9 +269,9 @@ GetMutectVAF <-function(vcf) {
   }
 
   if (all(type1 %in% unlist(strsplit(vcf$FORMAT[1], ":")))) {
-    return(GetVAFs(type1, vcf$FORMAT, vcf[, 10]))
+    return(GetVAFs(type1, vcf$FORMAT, vcf[[10]]))
   } else if (all(type2 %in% unlist(strsplit(vcf$FORMAT[1], ":")))) {
-    return(GetVAFs(type2, vcf$FORMAT, vcf[, 10]))
+    return(GetVAFs(type2, vcf$FORMAT, vcf[[10]]))
   }
 }
 
@@ -529,7 +529,7 @@ MakeVCFDBSdf <- function(DBS.range.df, SBS.vcf.dt) {
 #'
 #' @keywords internal
 SplitStrelkaSBSVCF <- function(vcf.df, max.vaf.diff = 0.02) {
-  stopifnot(class(vcf.df) == "data.frame")
+  stopifnot("data.frame" %in% class(vcf.df))
 
   # Record the total number of input variants for later sanity checking.
   num.in <- nrow(vcf.df)