[Bioc-sig-seq] GenomicFeatures package

[pterry at huskers.unl.edu]

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?

Thanks,
P. Terry
pterry at huskers.unl.edu