[BioC] Extend GRanges start/end
pshannon at fhcrc.org
Mon Oct 29 16:30:39 CET 2012
GenomicFeatures::promoters really is there. Truly! Your sessionInfo () results did not come through. Could you try that again?
All that said, Michael's suggestion of IRanges::resize may be a better fit to your problem, since you already have the full range of the gene
On Oct 29, 2012, at 7:53 AM, António Miguel de Jesus Domingues wrote:
> Thank you for your reply Paul.
> I had only read the vignette and should have read also the reference manual. That said it is still not working. The example:
> gr <- GRanges("chr1", IRanges(rep(10, 3), width=6), c("+", "-", "*"))
> promoters(gr, 2, 2)
> Gives and error:
> Error: could not find function "promoters"
> I've updated the GenomicRanges to 1.10.0 (sessionInfo bellow). Also from what I've read in the reference manual, "promoter" will return the region around the TSS: "The return object is a GRanges of promoter regions around the transcription start site the span of which is deﬁned by upstream and downstream. Ranges on the * strand are treated the same as those on the + strand.", something like upstream.TSS.downstream (very similar to the function flank), whereas I am interested in extending the range to something like upstream+FullGene. Please correct me if I am wrong.
> On another note, did the behaviour of transcriptsBy(hg19RefGenes, by='gene') changed in the last update? I thought the output was GRanges object but now it is a GRangesList.
> Best regards,
> On 29 October 2012 13:55, Paul Shannon <pshannon at fhcrc.org> wrote:
> Hi Antonio,
> New methods in Genomic Features 1.10.0
> might help you out here. The latter uses the former, and a documented example can be found here:
> If this is insufficient please let us know, and we can dig further into your problem.
> - Paul
> António Miguel de Jesus Domingues, PhD
> Neugebauer group
> Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
> Pfotenhauerstrasse 108
> 01307 Dresden
> e-mail: domingue at mpi-cbg.de
> tel. +49 351 210 2481
> The Unbearable Lightness of Molecular Biology
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