Update rc.qc.R

add flexibility to enable searching for qc.tag in specific column by allowing qc.tag to be a vector of length 2, c('tag', 'pheno.column')
cbroeckl · May 8, 2024 · 27c7aa9 · 27c7aa9
1 parent 62436b3
commit 27c7aa9
Showing 1 changed file with 11 additions and 3 deletions.
diff --git a/R/rc.qc.R b/R/rc.qc.R
@@ -53,11 +53,19 @@ rc.qc<-function(ramclustObj=NULL,
       stop("no tag provided", "\n")
     }
 
-    samples <- grep(tag[1], ramclustObj$phenoData$sample.names)
-    samples <- samples[which(samples <= nrow(ramclustObj$MSdata))]
+    if(length(tag) == 1) {
+      samples <- grep(tag[1], ramclustObj$phenoData$sample.names)
+      samples <- samples[which(samples <= nrow(ramclustObj$MSdata))]
+    }
+
+    if(length(tag) == 2) {
+      samples <- grep(tag[1], ramclustObj$phenoData[,tag[2]])
+      samples <- samples[which(samples <= nrow(ramclustObj$MSdata))]
+    }
+
 
     if (length(samples) == 0) {
-      stop("no ", tag, " samples found using the tag ", "'", tag, "'", "\n")
+      stop("no QC samples found using the tag ", "'", tag, "'", "\n")
     }
     return(samples)
   }