[BioC] Reading gff files in R

[Tobias Straub]

hi Naira
just parse the gff with

read.delim("gff_file.gff", header=F, comment.char="#") -> gff

and you get a table that you can filter for gene entries, sth like
gff.genes <- gff[gff[,2]=="gene",]
depending on  where and how the gene is specified as a gene

T.

On Oct 21, 2008, at 11:00 AM, Naira Naouar wrote:

> Dear all,
>
> I was wondering if there were already tools to read gff files in R?
> I am looking for a fast way to extract gene coordinates from a gff  
> file.
>
> Regards,
> Naira
>
> -- 
> ==================================================================
> Naïra Naouar
> Tel:+32 (0)9 331 38 63
> VIB Department of Plant Systems Biology, Ghent University
> Technologiepark 927, 9052 Gent, BELGIUM
> nanao at psb.ugent.be                         http://www.psb.ugent.be
>
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Tobias Straub   ++4989218075439   Adolf-Butenandt-Institute, München D