I think I fixed this one, version 1.1.13.

Michael

On Sat, Jun 12, 2010 at 12:34 AM, Dario Strbenac
<D.Strbenac@garvan.org.au>wrote:

> 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
>
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>

	[[alternative HTML version deleted]]

