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

Zhu, Lihua (Julie) Julie.Zhu at umassmed.edu
Fri Aug 29 22:12:31 CEST 2014


Thanks for reporting the bug in function peaksNearBDP!  Jianhong has fixed it and the new version is 2.14.1 (revision 93700).

Best regards,


On 8/26/14 2:42 AM, "Preussner, Jens" <Jens.Preussner at mpi-bn.mpg.de> wrote:

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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