[BioC] ChIPpeakAnno: Invalid row.names length in peaksNearBDP

Preussner, Jens Jens.Preussner at mpi-bn.mpg.de
Tue Aug 26 08:42:15 CEST 2014

Dear Julie,

I noticed an unwanted breaking of the peaksNearBDP function in your package. When searching for bidirectional promoters in annotationData that contains just one entry, the function gives an "invalid row.names error". Is this intended?

Just for completeness and reproducability, I used the following code:

peaks = BED2RangedData(file.path("test.bed"),header=F)
annotation = GFF2RangedData(file.path("ref.gtf"),header=F,comment.char="#",sep="\t")
ovl_data = peaksNearBDP(peaks, AnnotationData = annotation, MaxDistance = 3000, PeakLocForDistance = "middle", FeatureLocForDistance = "TSS")

The two files are attached.
Thanks for your time and best regards,

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