[BioC] all human gene coordinates

[Steve Lianoglou]

Hi,

On Thu, Dec 13, 2012 at 11:20 AM, Wim Kreinen <wkreinen at gmail.com> wrote:
> Thanks,
>
> is there a method to get all protein coding transcripts. With your method I
> get microRNAs as well.

Here's one non-sophisticated way. The idea is to get the info for all
coding exons grouped by tx_id, then filter the transcript list by ids
that appear in the coding-exon list names:

R> library("TxDb.Hsapiens.UCSC.hg19.knownGene")
R> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
R> txs <- transcripts(txdb)
R> cds <- cdsBy(txdb)
R> txs.coding <- txs[mcols(txs)$tx_id %in% names(cds)]

HTH,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact