The GenomicFeatures package has transcript information from the UCSC
database.

library(GenomicFeatures)
data(geneHuman)

## filter for reads in hg18 chr1 promoter regions (by default, -500,500 of
TSS)

trans <- transcripts(geneHuman)
promoters <- Views(cov, trans["chr1"]$promoter)
viewSums(promoters)

## trans also includes whole transcript, upstream, downstream and threeprime
regions
## you can do the same for introns, exons
introns <- Views(cov, ranges(introns(geneHuman))[[1]])
exons <- Views(cov, ranges(exons(geneHuman))[[1]])

Michael

On Tue, Aug 25, 2009 at 10:41 PM, Bogdan Tanasa <tanasa@gmail.com> wrote:

> Hi everyone,
>
> to add another question - I would highly appreciate if you could let me
> know
>
> any quick way to obtain the ChIP-seq tag density plots in the vicinity of
> various
> genomic elements - eg promoters, introns, or given a custom list ? thanks
> again.
>
> -- bogdan
>
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>
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