On Fri, Oct 16, 2009 at 2:58 PM, Chris Seidel <seidel@phaget4.org> wrote:

> Hello,
>
> I'm getting an error using export() to generate a wig file from a
> coverage result.
>
> In an earlier thread (Subject: Re: [Bioc-sig-seq] WIG from coverage, Sep
> 30, 2009 at 3:15 PM) there was an example of going from reads to
> coverage to wig, and Michael Lawrence had suggested:
>
> > The most convenient path would be to perform the analysis over all
> > chromosomes and lanes at once. The extendReads() function should do
> this for
> > you, e.g:
> >
> > extendedReads <- extendReads(ypd, seqLen=150)
> >
> > The 'extendedReads' above is a GenomeDataList. You could then do
> something
> > like:
> >
> > cov <- gdapply(extendedReads, coverage)
> >
> > Now 'cov' is another GenomeDataList. Just subset out one lane and export
> > it:
> >
> > export(cov$wce, "wce.wig")
>
> When I try this, I get an error:
>
> # read in data and convert to genome data objects
> aln <- readAligned(spath, pattern="s_1_export.txt", type="SolexaExport",
> filter=filt)
> ip <- as(aln,"GenomeData")
> aln <- readAligned(spath, pattern="s_2_export.txt", type="SolexaExport",
> filter=filt)
> wce <- as(aln,"GenomeData")
>
> # create GenomeDataList from ip and wce
> cb <- GenomeDataList(list(ip=ip, wce=wce))
>
> # extend reads
> cb.ext <- extendReads(cb, seqLen=50)
>
> # get coverage for both lanes across all chromosomes
> cb.cov <- gdapply(cb.ext, coverage)
>
> # export the ip lane to wig
> export(cb.cov$ip, "cb_ip.wig")
>
> Error in object[order(start(object)), ] :
>    cannot combine 'i' row values from different spaces
>
> However, it works correctly if I "export" one chromosome at a time:
>
> export(cb.cov$ip$chr2L, "cb_ip.wig")
>
> Is this a bug, or am I doing something wrong? Can export take a
> subsetted GenomeDataList object? I even tried coercing the GenomeData
> element to RangedData, but I got the same error while trying to export.
>
>
This is a bug in rtracklayer, fixed in version 1.5.23.



> -Chris Seidel
>
> > sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-09-03 r49555)
> x86 <- 64-unknown-linux-gnu
>
> other attached packages:
>  [1] rtracklayer <- 1.5.17 RCurl <- 1.2-0        bitops <- 1.0-4.1
> chipseq <- 0.1.27
> [5] ShortRead <- 1.3.36   lattice <- 0.17-25    BSgenome <- 1.13.14
> Biostrings <- 2.13.47
> [9] IRanges <- 1.3.87
>
> loaded via a namespace (and not attached):
>  [1] Biobase <- 2.5.8 XML <- 2.6-0     grid <- 2.10.0   hwriter <- 1.1
>  tools <- 2.10.0
>
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>

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