I believe you Paul. I just realized that I needed to re-start R after the
update :)

Now all I have to do is modify my script with the re-named functions.
Thanks a lot for your help. Just one näive
question/suggestion/brainstorming: why isn't there a function to extract
all the continuously transcribed regions of the genome (= Genes)? Is it
because it is something hard to define and thus it is left to individual
users to choose which approach to take (making them aware of the caveats)?

António


On 29 October 2012 16:30, Paul Shannon <pshannon@fhcrc.org> wrote:

> 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@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@mpi-cbg.de
> > tel. +49 351 210 2481
> > The Unbearable Lightness of Molecular Biology
>
>


-- 
-- 
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@mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology

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