Thanks,

is there a method to get all protein coding transcripts. With your method I
get microRNAs as well.
Thanks
Wim

2012/12/5 Steve Lianoglou <mailinglist.honeypot@gmail.com>

> Hi Wim,
>
> Please keep emails on the bioc list by hitting "reply all" -- this way
> you can get more (and better help) by having more eyes on your
> question, and also others can benefit as well.
>
> So:
>
> On Wed, Dec 5, 2012 at 11:29 AM, Wim Kreinen <wkreinen@gmail.com> wrote:
> > This sounds promising.
> > And principally I understand how it works but ... How do I define keys
> if I
> > want all transcripts?
> >  I defined via isActiveSeq the chr1...chr22, chrX, chrY as active
> > chromosomes.
> >
> > I tried
> > library ("TxDb.Hsapiens. UCSC.hg19.knownGenes")
> > txdb->TxDb.Hsapiens. UCSC.hg19.knownGenes
> > cols->c("TXCHROM", "TXSTRAND", "TXSTART", "TXEND")
> > keys -> ? #How do I define keys if I want all transcripts?
> > alltranscripts->select (txdb, keys=keys, cols=cols, keytype="TXID")
>
> First: what's up w/ the spaces in your "TxDb.Hsapiens.[SPACE]UCSC..."
>
> It's also ...knownGene -- not ...knownGeneS
>
> Also, a suggestion: use `<-` for assignment, and not `->` ... although
> the latter works, if anybody else is meant to read your code, they're
> likely going to be confused for a bit until they get used to your
> "odd" (but correct) choice of assignment direction.
>
> Anyhow -- how about:
>
> R> library(BiocInstaller)
> R> biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
> R> library("TxDb.Hsapiens.UCSC.hg19.knownGene")
> R> txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
> R> txs <- transcripts(txdb)
> R> head(txs)
> R> head(txs)
> GRanges with 6 ranges and 2 metadata columns:
>       seqnames           ranges strand |     tx_id     tx_name
>          <Rle>        <IRanges>  <Rle> | <integer> <character>
>   [1]     chr1 [ 11874,  14409]      + |         1  uc001aaa.3
>   [2]     chr1 [ 11874,  14409]      + |         2  uc010nxq.1
>   ...
>
> the ucsc id's are in the tx_name column.
>
> 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
>

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