On Fri, Oct 16, 2009 at 2:58 PM, Chris Seidel <[email protected]> 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 > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
