Hi,

Your BED file contains a "track line" which is something that is defined by
the UCSC Genome Browser. I view (and others might disagree, in fact I often
disagree with myself about this) that the track lines are specific to UCSC
and not in the core BED format. Thus when rtracklayer sees a track line, it
by default attempts to make the chromosomes conform to the UCSC convention.

This can be avoided in a number of ways. First, passing trackLine=FALSE will
cause the track line to be ignored. Second, passing asRangedData=FALSE will
cause the return value to be a GRanges, in which case it cannot hold the
track line data (at least not in any formal way -- it could go into the
metadata) and thus the track line is ignored.

So those are workarounds. I could be convinced though that presence of a
track line does NOT imply conformance to UCSC conventions.

I fixed the incomplete conversion in devel. Please let me know if it needs
to be back-ported.

Michael

On Tue, May 31, 2011 at 12:53 PM, Cook, Malcolm <MEC@stowers.org> wrote:

> I find that rtracklayer's import.bed function is pasting the string 'chr'
> to SOME of my chromosome names in my bed file ( f, attached)
>
> It is as if it is trying to rename (some) of them to (partially) agree with
> ucsc's naming convention.
>
> I would expect import.bed  to preserve column 1 as the name of the 'space',
> but it does not.
>
> But... some of the spaces have had a 'chr' prefix added!
>
> Look at the session transcipt below!
>
> I _think_ this behavior is NEW since I recently upgraded.
>
> I hope not to have to revert to previous version of R / bioconductor to
> address this issue.
>
> Any suggestions?
>
> Thanks!
>
> Malcolm Cook
> Computational Biology - Stowers Institute for Medical Research
>
>
>
>
> > library(rtracklayer)
> Loading required package: RCurl
> Loading required package: bitops
> > unique(read.table('f.bed',sep="\t",skip=1)[,1])
>  [1] YHet                      dmel_mitochondrion_genome
>  [3] 2L                        X
>  [5] 3L                        4
>  [7] 2R                        3R
>  [9] Uextra                    2RHet
> [11] 2LHet                     3LHet
> [13] 3RHet                     U
> [15] XHet
> 15 Levels: 2L 2LHet 2R 2RHet 3L 3LHet 3R 3RHet 4 U Uextra X XHet ...
> dmel_mitochondrion_genome
> > unique(space(import.bed ('f.bed')))
>  [1] chr2L                     2LHet
>  [3] chr2R                     2RHet
>  [5] chr3L                     3LHet
>  [7] chr3R                     3RHet
>  [9] chr4                      chrU
> [11] Uextra                    chrX
> [13] XHet                      YHet
> [15] dmel_mitochondrion_genome
> 15 Levels: chr2L 2LHet chr2R 2RHet chr3L 3LHet chr3R 3RHet chr4 chrU ...
> dmel_mitochondrion_genome
> > sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rtracklayer_1.12.2 RCurl_1.5-0        bitops_1.0-4.1
>
> loaded via a namespace (and not attached):
> [1] BSgenome_1.20.0     Biostrings_2.20.1   GenomicRanges_1.4.6
> [4] IRanges_1.10.4      XML_3.4-0
> >
>
>
>

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