fix getMarkers3

RNASeq.R

@@ -1161,20 +1161,6 @@ getMarkers<-function(expressionMatrix,annotation){
 }
 
 
-getMarkers2<-function(expressionMatrix,group){
-	require(ROCR)
-	group<-as.factor(group)
-	group<-droplevels(group)
-	binaryGroup<-vapply(levels(group),function(x){
-		as.numeric(x==group)
-	},FUN.VALUE = numeric(length(group)))
-	apply(binaryGroup,2,function(labels){
-		apply(expressionMatrix,1,function(x){
-			performance(prediction(x,labels),"auc")@y.values[[1]]
-		})
-	})
-}
-
 # By Miron Kursa https://mbq.me
 auroc <- function(score, bool) {
 	n1 <- sum(!bool)
@@ -1198,28 +1184,28 @@ getMarkers2<-function(expressionMatrix,group){
 }
 
 
-getMarkers3<-function(expressionMatrix,group){
-	require(BiocParallel)
-	BPPARAM=bpparam()
-	if(!is.matrix(expressionMatrix)) expressionMatrix<-as.matrix(expressionMatrix)
-	if(length(group)!=ncol(expressionMatrix)) stop("group should be a vector with same length as number of column in expressionMatrix")
-	
-	group<-as.factor(group)
-	group<-droplevels(group)
-	binaryGroup<-lapply(levels(group),function(x){
-		x==group & !is.na(group)
-	});names(binaryGroup)<-levels(group)
-	
-	res<-as.matrix(data.frame(lapply(binaryGroup,function(labels){
-		unlist(bplapply(seq_len(nrow(expressionMatrix)),function(i,expressionMatrix,labels){
-			auroc(expressionMatrix[i,],labels)
-		},labels=labels,expressionMatrix=expressionMatrix,BPPARAM = BPPARAM),recursive = FALSE)
-	})))
-	rownames(res)<-rownames(expressionMatrix)
-	res
-	
+getMarkers3<-function(expressionMatrix,group,BPPARAM=NULL){
+  require(BiocParallel)
+  if(is.null(BPPARAM )) BPPARAM=bpparam()
+  if(!is.matrix(expressionMatrix)) expressionMatrix<-as.matrix(expressionMatrix)
+  if(length(group)!=ncol(expressionMatrix)) stop("group should be a vector with same length as number of column in expressionMatrix")
+  
+  group<-as.factor(group)
+  group<-droplevels(group)
+  binaryGroup<-lapply(levels(group),function(x){
+    x==group & !is.na(group)
+  });names(binaryGroup)<-levels(group)
+  
+  res<-as.matrix(data.frame(lapply(binaryGroup,function(labels){
+    unlist(bplapply(seq_len(nrow(expressionMatrix)),function(i,expressionMatrix,labels,auroc){
+      auroc(expressionMatrix[i,],labels)
+    },labels=labels,expressionMatrix=expressionMatrix,auroc=auroc,BPPARAM=BPPARAM),recursive = FALSE)
+  })))
+  rownames(res)<-rownames(expressionMatrix)
+  res
 }
 
+
 corGeneToOthers<-function(gene,expression,corFun=cor,...){
 	expression<-as.matrix(expression)
 	t(corFun(expression[gene,],t(expression),...))[,1]