[BioC] GenomicRanges countOverlaps error

[Suraj Menon]

Hi all

I've been trying to use the GenomicRanges countOverlaps function. When I was using the release version of GenomicRanges, countOverlaps worked fine for coordinates from chromosomes 1-9, but gave me an error for the others. 

I switched to using the development version of GenomicRanges. The function now works for all chromosomes other than X and Y.
Does anyone know a way around this?
(see code below)

> aligns <- readBamGappedAlignments(testFile)
> rname(aligns)
'factor' Rle of length 29420299 with 75 runs
  Lengths: 520361 542488 405709 384155 391181 ... 143664   2162 587871  40505
  Values :   chr1   chr2   chr3   chr4   chr5 ...  chr22   chrM   chrX   chrY
Levels(49): chr1 chr10 chr10_random chr11 ... chrM chrX chrX_random chrY
> yst <- seq(1, 1000, by=100)
> ywd <- rep(100, length(yst))
> ## chr1
> gr <- GRanges(seqnames = Rle("chr1", length(yst)),
+      ranges = IRanges(yst, width = ywd))
> counts <- countOverlaps(gr, aligns)
> counts
 [1]  0 14 11  1  8 12  2  0  0  0
>
> ## chr18
> gr <- GRanges(seqnames = Rle("chr18", length(yst)),
+      ranges = IRanges(yst, width = ywd))
> counts <- countOverlaps(gr, aligns)
> counts
 [1]  2 31  1  4  4  4  8  5  6  3
>
> ## chrX
> gr <- GRanges(seqnames = Rle("chrX", length(yst)),
+      ranges = IRanges(yst, width = ywd))
> counts <- countOverlaps(gr, aligns)
Warning message:
In .local(query, subject, maxgap, minoverlap, type, select, ...) :
  'query' and 'subject' do not use a similiar naming convention for seqnames
>
> ## chrY
> gr <- GRanges(seqnames = Rle("chrY", length(yst)),
+      ranges = IRanges(yst, width = ywd))
> counts <- countOverlaps(gr, aligns)
Warning message:
In .local(query, subject, maxgap, minoverlap, type, select, ...) :
  'query' and 'subject' do not use a similiar naming convention for seqnames
>
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] Rsamtools_1.0.8      Biostrings_2.17.26   GenomicRanges_1.1.25
[4] IRanges_1.7.32

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 tools_2.11.1


Cheers
-Suraj

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