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List:       bioconductor
Subject:    Re: [BioC] Finding TSS locations
From:       Moiz Bootwalla <msbootwalla () gmail ! com>
Date:       2012-06-27 14:13:40
Message-ID: 456FA530-0775-4848-8049-7C773497A352 () gmail ! com
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Hi Tom,

Continuing with the previous code snippet, here's how you can create a named vector \
of TSS locations, where the names are the Entrez IDs.

tss.vector <- start(tss)
names(tss.vector) <- values(tss)$tx_id

That should do it. If you plan on working more with GRanges objects you should spend \
some time working through the GenomicRanges vignette. It will prove to be a great \
investment. 

Regards,
Moiz


On Jun 27, 2012, at 6:51 AM, Bartlett, Thomas wrote:

> Hi Moiz,
> 
> Thanks again for your help with this, and sorry if this is a stupid question(!), \
> but how do I convert the tss S4 object into, say, a named vector, or a 2-column \
> matrix, which links e.g., Entrez ID to TSS location of the corresponding gene? 
> best wishes
> 
> Tom
> 
> From: Moiz Bootwalla [msbootwalla@gmail.com]
> Sent: 27 June 2012 09:49
> To: Bartlett, Thomas
> Cc: bioconductor@r-project.org
> Subject: Re: [BioC] Finding TSS locations
> 
> Hi Thomas,
> 
> The following code snippet gets the tss for all genes based on the UCSC refGene \
> table using GenomicFeatures. 
> refgene <- makeTranscriptDbFromUCSC(genome="hg19", tablename="refGene")
> transcripts <- transcripts(refgene, columns=c("tx_id", "tx_name"))
> tss <- resize(transcripts, width=1, fix='start')
> 
> You should probably save the TranscriptDB object using saveFeatures() so that you \
> do not have to recreate it the next time you need it. Refer to the GenomicFeatures \
> vignette on how to do that. 
> Hope this helps.
> 
> Moiz
> 
> 
> 
> On Jun 27, 2012, at 1:26 AM, Bartlett, Thomas wrote:
> 
> > Hi,
> > 
> > I'm trying to find a way to get the locations of the tss (transcriptional start \
> > site) for genes (I need this for work analysising Illumina 450K methylation \
> > data). I've tried the package GenomicFeatures, and have successfully downloaded \
> > and loaded the package, however the relevant command data(geneHuman) doesn't seem \
> > to work, producing the following error message: Warning message:
> > In data(geneHuman) : data set ‘geneHuman’ not found
> > 
> > I'm currently using R 2.15 on Windows Vista (I also have access to a Unix-type \
> > machine) 
> > thanks in advance for your help
> > 
> > Tom Bartlett
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: \
> > http://news.gmane.org/gmane.science.biology.informatics.conductor


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