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

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]]