Dear Julie,

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:

library(“ChIPpeakAnno”)

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)

TRUE

Thanks and best regards,

Jens

Edit: Files are available as gist:

Dear Jens,

It is intended. You will notice that there is no annotation added to the peaks without overlap.  This function is intended for annotating peaks. If you are interested in finding overlapping peaks only, I suggest you use function findOverlappingPeaks. For example, t1 <-   findOverlappingPeaks(peaks1, peaks2, maxgap=1000, NameOfPeaks1="TF1", NameOfPeaks2="TF2", select="all", annotate=1) 
r = t1$OverlappingPeaks

Best, 

Julie