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 <[email protected]> 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
