On Mon, Oct 29, 2012 at 3:37 AM, António Miguel de Jesus Domingues <
amjdomingues@gmail.com> 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")
>

You should be able to simply call range() on GeneRegions, i.e., no need to
call seqapply. Btw, what is the progress="text" argument here? I'm not
aware of this feature.


> 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 ?
>
>
resize() should work. Simply call resize(GeneRegions, width(GeneRegions) +
1000L, fix = "end").

Michael


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