[BioC] exonsBy() function from GenomicFeature, preserve transcript names?

[Paul Geeleher]

Hi Marc,

Thank you for your reply. I was trying to get this done using an older
version of R that happened to be running on our cluster,
GenomicFeatures has been updated and everything is sorted now.

Thanks!

Paul.

On Thu, Jan 20, 2011 at 11:53 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> Hi Paul,
>
> If you are using a current enough version of GenomicFeatures then this
> will do something like that:
>
> eaTx <- exonsBy(hgTxDb, 'tx', use.names=TRUE)
>
> I can't tell if this will help you though since you did not post
> sessionInfo().  If it doesn't work, then you can also use exons() and
> get the data by requesting "tx_name" for the columns argument.
>
>
>  Marc
>
>
>
> On 01/20/2011 11:36 AM, Paul Geeleher wrote:
>> Hi,
>>
>> I've noticed when I use exonsBy() to download exons by transcript like this:
>>
>> library(GenomicFeatures)
>> hgTxDb <- makeTranscriptDbFromUCSC(genome="hg18", tablename="ensGene")
>> eTx <- exonsBy(hgTxDb, 'tx')
>>
>> That the object returned (eTx in this case) doesn't contain the
>> transcript names. But if we use
>>
>> e <- exonsBy(hgTxDb, 'gene')
>>
>> The ensembl gene names are returned as the names of GRangesList "e".
>> I'm wondering if there's a convenient way of annotating the eTx object
>> with the transcript names also?
>>
>> Thanks,
>>
>> Paul.
>>
>>
>>
>
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-- 
Paul Geeleher (PhD Student)
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com