On Tue, Oct 27, 2009 at 3:53 PM, pterry@huskers.unl.edu <
pterry@huskers.unl.edu> wrote:

> Dear bioc-sig-sequencing,
>
> Previously, I tried the following with a UCSC available genome.
>
> genetable<-read.table("celegans_chrIII.txt", header=T, sep="\t")
> >
> promoter<-IRanges(start=genetable$txStart-1000*as.real(genetable$strand=="+"),
> width=1000)
>
> It was suggested I might "check out the GenomicFeatures package, which has
> utilities for working with a data.frame representation of the UCSC genes
> table. For example, the 'transcripts' function will give you a set of
> regions, including the promoters you're trying to generate."
>
> I have a genome, arabidopsis, apparently not available at the UCSC
> database, but rather from TAIR.
>
> For this genome, might the GenomicFeatures pakage be similarly helpful?  I
> assume one might start with a file like TAIR9_GFF3_genes.gff from the TAIR
> site?  I note it has records for 'gene', 'mRNA', 'CDS', 'exon', perhaps
> others?
>
>
It could be useful, but you'll need to get it into the shape expected by the
GenomicFeatures functions. With specific regard to transcripts(), it will
need a 'chrom' column with the chromosome names, 'name' column for the gene
name, and 'txStart' and 'txEnd' for the start and end of the transcripts,
using UCSC coordinate conventions.

I'm now thinking that it would be more convenient for the user if there was
a transcripts method on a RangesList object, which could provide the
necessary information. This could be extracted from the RangedData, which
rtracklayer can create from your GFF file, with one caveat: if the GFF file
contains a mixture of features (genes, exons, etc) and relies on the
hierarchical features of GFF, it will take more work to get things into the
right shape.

The question then is where would this new functionality belong? The future
of the GenomicFeatures package was a bit uncertain, the last time I checked.

Michael

Thanks,
> P. Terry
> pterry@huskers.unl.edu
>
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