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

[Marc Carlson]

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.
>
>
>