when using the annotatePeakInBatch function of your ChIPpeakAnno package with non-overlapping peaks and annotation, the resulting object equals the input peaks.
Is this intended? How would I know that there is no overlap then? I used a work-around with all(ovl == peaks) to check if the result contains the same entries as the peaks (see below).
Code to reproduce:
peaks = BED2RangedData(file.path(“peaks.bed”),header=F)
annotation = GFF2RangedData(file.path(“annotation.gff”),header=F,comment.char=”#”,sep=”\t”)
ovl = annotatePeakInBatch(peaks, AnnotationData = annotation, output = 'overlapping', maxgap = 0, select = "all", FeatureLocForDistance = "TSS")
all(ovl == peaks)
Thanks and best regards,
Edit: Files are available as gist: