[BioC] Extend GRanges start/end

[Paul Shannon]

Hi Antonio,

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

 - Paul


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("+", "-", "*"))
> gr
> 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,
> António 
> 
> 
> On 29 October 2012 13:55, Paul Shannon <pshannon at fhcrc.org> wrote:
> Hi Antonio,
> 
> New methods in Genomic Features 1.10.0
> 
>    promoter
>    getPromoterSeq
> 
> might help you out here.  The latter uses the former, and a documented example can be found here:
> 
>   http://www.bioconductor.org/help/workflows/gene-regulation-tfbs/#compact-summary
> 
> If this is insufficient please let us know, and we can dig further into your problem.
> 
> Cheers,
> 
>  - Paul
> 
> 
> -- 
> -- 
> António Miguel de Jesus Domingues, PhD
> Neugebauer group
> Max Planck Institute of Molecular Cell Biology and Genetics, Dresden
> Pfotenhauerstrasse 108
> 01307 Dresden
> Germany
> 
> e-mail: domingue at mpi-cbg.de
> tel. +49 351 210 2481
> The Unbearable Lightness of Molecular Biology