[BioC] Extend GRanges start/end

[Paul Shannon]

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

On Oct 29, 2012, at 3:37 AM, António Miguel de Jesus Domingues wrote:

> Hi Bioconducters,
> 
> I have a GRanges object created with the package  GenomicFeatures that
> contains gene coordinates:
> 
> ##########################################################
> hg19RefGenes <- loadFeatures(file='hg19RefGenes.sqlite')
> hg19RefGenes
> 
> # generate a GRanges object containing contiguous transcribed regions of
> the genome (from the 1st to last exon)
> GeneRegions <- transcriptsBy(hg19RefGenes, by='gene')
> gene.bounds <- seqapply(GeneRegions, range, progress="text")
> GeneRegions <- unlist(gene.bounds)
> head(GeneRegions)
> GRanges with 6 ranges and 0 elementMetadata cols:
>            seqnames                 ranges strand
>               <Rle>              <IRanges>  <Rle>
>          1    chr19 [ 58858172,  58864865]      -
>         10     chr8 [ 18248755,  18258723]      +
>        100    chr20 [ 43248163,  43280376]      -
>       1000    chr18 [ 25530930,  25757445]      -
>      10000     chr1 [243651535, 244006886]      -
>  100008586     chrX [ 49217771,  49342266]      +
>  ---
>  seqlengths:
>                    chr1                  chr2 ... chr18_gl000207_random
>               249250621             243199373 ...                  4262
> ##########################################################
> 
> I want to do something that should be simple: extend the ranges to that it
> also includes 1Kb upstream of the gene (~Promoter region), for example,
> chr19 [ 58858172,  58864865] becomes chr19 [ 58858172,  58865865]. Looking
> at the GenomicFeatures fucntions it seems that neither resize or flank will
> do. Is there another function that I am missing that will do the job ?
> 
> Cheers,
> António
> 
> -- 
> -- 
> 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
> 
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> 
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