Question: ChIPpeakAnno: Invalid row.names length in peaksNearBDP
0
gravatar for Jens Preussner
4.9 years ago by
Germany
Jens Preussner30 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: library("ChIPpeakAnno") 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, Jens
annotation annotationdata • 634 views
ADD COMMENTlink modified 4.9 years ago by Julie Zhu4.0k • written 4.9 years ago by Jens Preussner30
Answer: ChIPpeakAnno: Invalid row.names length in peaksNearBDP
1
gravatar for Julie Zhu
4.9 years ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k wrote:
Jens, Thanks for reporting the bug in function peaksNearBDP! Jianhong has fixed it and the new version is 2.14.1 (revision 93700). Best regards, Julie 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: library("ChIPpeakAnno") 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, Jens [[alternative HTML version deleted]]
ADD COMMENTlink written 4.9 years ago by Julie Zhu4.0k
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