add logical option for define_samples

optional logical output, with vector sample length as phenoData/MSdata rows.

R/rc.feature.filter.cv.R

@@ -32,10 +32,12 @@ check_arguments_filter.cv <- function(ramclustObj, qc.tag) {
 #'
 #' @param ramclustObj ramclustObj containing MSdata with optional MSMSdata (MSe, DIA, idMSMS)
 #' @param tag character vector of length one or two.  If length is two, enter search string and factor name in $phenoData slot (i.e. c("QC", "sample.type"). If length one (i.e. "QC"), will search for this string in the 'sample.names' slot by default.
+#' @param logical optionally convert numeric vector with length equal to the number of matched samples to a logical vector of length equal to number of samples, with TRUE representing matching samples. 
+#' 
 #' @return samples found using the tag
 #' @export
 
-define_samples <- function(ramclustObj, tag) {
+define_samples <- function(ramclustObj, tag, logical = FALSE) {
   ## define samples in each set
   if(length(tag) == 0) {
     stop("no tag provided", "\n")
@@ -55,6 +57,11 @@ define_samples <- function(ramclustObj, tag) {
   if (length(samples) == 0) {
     stop("no QC samples found using the tag ", "'", tag, "'", "\n")
   }
+
+  if(logical) {
+    1:nrow(ramclustObj$MSdata) %in% samples
+  }
+
   return(samples)
 }
 

R/rc.feature.normalize.qc.R

@@ -78,7 +78,8 @@ rc.feature.normalize.qc <- function(ramclustObj = NULL,
 
   ## define QC samples in each set
   if(!is.null(qc.tag)) {
-    qc <- grepl(qc.tag[1], ramclustObj$phenoData[,2])
+    # qc <- grepl(qc.tag[1], ramclustObj$phenoData[,2])
+    qc <- define_samples(ramclustObj = ramclustObj, tag = qc.tag, logical = TRUE)
   }
 
   if (!is.logical(qc)) {