fix the ifelse for novel Tx

suiyue · suiyue · commit 2371bd6ca838 · 2025-02-03T13:48:07.000+08:00
diff --git a/R/readWrite.R b/R/readWrite.R
@@ -249,7 +249,7 @@ writeAnnotationsToGTF <- function(annotation, file, geneIDs = NULL, outputExtend
     }
 
     if(outputNovelOnly){
-        if(all(!rowData(se)$novelTranscript)){
+        if(all(!mcols(annotation)$novelTranscript)){
           print("This is no novel transcript and novelTranscripts.gtf will not be outputed!")
         }
       else{

Original file line number	Diff line number	Diff line change
`@@ -249,7 +249,7 @@ writeAnnotationsToGTF <- function(annotation, file, geneIDs = NULL, outputExtend`
`249`	`249`	`}`
`250`	`250`
`251`	`251`	`if(outputNovelOnly){`
`252`		`- if(all(!rowData(se)$novelTranscript)){`
	`252`	`+ if(all(!mcols(annotation)$novelTranscript)){`
`253`	`253`	`print("This is no novel transcript and novelTranscripts.gtf will not be outputed!")`
`254`	`254`	`}`
`255`	`255`	`else{`