[Bioc-sig-seq] GenomicRanges findOverlaps error message

[Dario Strbenac]

Hello,

I have both the query and subject seqnames in the same naming format, yet I still get an error. Could this be a bug ? I have GenomicRanges_1.0.3 loaded.

> crossMatch <- findOverlaps(gr, genoFeatures)
Error in .local(query, subject, maxgap, minoverlap, type, select, ...) : 
  'query' and 'subject' do not use a similiar naming convention for seqnames
> table(seqnames(gr))

    chr10 
135374737 
> table(seqnames(genoFeatures))

 chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19  chr2 chr20 
67731 30782 39027 39401 11943 20718 24489 28618 40905 10309 40218 52690 17253 
chr21 chr22  chr3  chr4  chr5  chr6  chr7  chr8  chr9  chrX  chrY 
 8740 15644 40959 26560 30281 33647 34001 24731 27650 32215  3878

I ran through gr having coordinates from chr1 to chr9 fine, it's just when gr got to containing coordinates from chr10, that it crashes.

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia