On Tue, Mar 16, 2010 at 5:25 PM, Jason Lu <[email protected]> wrote:
> Hi Patrick, > Yes. I would like to do something as Sean said. You are right that in > my SimpleRleList, the elements are ensembl transcript ids, and the > values are coverages. > > You'll want to get your SimpleRleList into something range-based, like a RangedData. as(x, "RangedData") will give you one, with your coverage in the 'score' variable. Then you could shift the ranges in the RangedData. > My purpose is to convert the ranges to the genomic coordinates (no > need to map to UCSC genes). I have the exon_start and exon_end > position by using biomaRt. I would like to do something like shift, > but not sure if it will work (since I need to keep track of the strand > info and all exon start positions). Currently I wrote a python script > to do this, but also want to do it in R directly. > > Thanks all for being helpful. > > Jason > > > > On Tue, Mar 16, 2010 at 6:25 PM, Patrick Aboyoun <[email protected]> > wrote: > > I'm not so sure the shift operator will do the trick since we don't have > a > > mapping of Ensembl transcripts to UCSC known gene transcripts. Also what > is > > stored in the SimpleRleList object. Are the elements transcripts and do > the > > values represent coverage? > > > > > > Patrick > > > > > > > > On 3/16/10 1:53 PM, Michael Lawrence wrote: > > > > So to summarize, Jason needs to use GenomicFeatures to get the ensembl > exons > > out, get the start positions, and use them to shift his ranges. > > > > On Tue, Mar 16, 2010 at 1:37 PM, Patrick Aboyoun <[email protected]> > wrote: > >> > >> The GenomicFeatures package in BioC 2.6 (w/ R-devel) supports the > >> following set of transcript tables provided by UCSC: > >> > >> track subtrack > >> knownGene UCSC Genes <NA> > >> knownGeneOld3 Old UCSC Genes <NA> > >> wgEncodeGencodeManualRel2 Gencode Genes Genecode Manual > >> wgEncodeGencodeAutoRel2 Gencode Genes Genecode Auto > >> wgEncodeGencodePolyaRel2 Gencode Genes Genecode PolyA > >> ccdsGene Consensus CDS <NA> > >> refGene RefSeq Genes <NA> > >> xenoRefGene Other RefSeq <NA> > >> vegaGene Vega Genes Vega Protein Genes > >> vegaPseudoGene Vega Genes Vega Pseudogenes > >> ensGene Ensembl Genes <NA> > >> acembly AceView Genes <NA> > >> sibGene SIB Genes <NA> > >> nscanPasaGene N-SCAN N-SCAN PASA-EST > >> nscanGene N-SCAN N-SCAN > >> sgpGene SGP Genes <NA> > >> geneid Geneid Genes <NA> > >> genscan Genscan Genes <NA> > >> exoniphy Exoniphy <NA> > >> augustusHints Augustus Augustus Hints > >> augustusXRA Augustus Augustus De Novo > >> augustusAbinitio Augustus Augustus Ab Initio > >> acescan ACEScan <NA> > >> > >> > >> Patrick > >> > >> On 3/16/10 1:18 PM, Michael Lawrence wrote: > >> > I think his problem is not access to UCSC but retrieving the exon > >> > locations. The transformation of the coordinate systems is a simple > >> > shift() call, once you have the exons. I don't know about Ensembl, but > >> > the GenomicFeatures package provides the UCSC predictions. > >> > > >> > I just realized yesterday that all of the gene predictions stored > >> > within UCSC have the same, documented table format. Presumably > >> > rtracklayer could convert these into something like what is provided > >> > by GenomicFeatures, but I think GenomicFeatures already has a function > >> > for doing that (building the DB). Could the utilities in > >> > GenomicFeatures be slightly generalized to support the alternative > >> > gene predictions in UCSC? > >> > > >> > Sorry for sort of hijacking the thread... > >> > > >> > Michael > >> > > >> > On Tue, Mar 16, 2010 at 11:20 AM, Patrick Aboyoun <[email protected] > >> > <mailto:[email protected]>> wrote: > >> > > >> > Jason, > >> > The rtracklayer provides an interface to the UCSC browser. In > >> > particular rtracklayer::export can export a SimpleRleList to a bed > >> > file that you can upload to UCSC. > >> > > >> > Patrick > >> > > >> > > >> > > >> > On 3/16/10 6:50 AM, Jason Lu wrote: > >> > > >> > Hi, > >> > > >> > I would like get suggestions on what is the best way to do > this. > >> > I > >> > have a "SimpleRleList" object, in which the range coordinates > >> > are > >> > relevant to an ensembl transcript (ranges from 1 to the total > >> > length > >> > of the transcript). I would like to show my data on the UCSC > >> > browser, > >> > so I need to map those coordinates to the genome. Currenty I > >> > wrote my > >> > own script to do this, based on the exon locations from > >> > biomart. There > >> > got to be an easy way to do this, but don't seem to find a > quick > >> > answer. Sorry if this has been answered. > >> > > >> > Thanks. > >> > > >> > Jason > >> > > >> > _______________________________________________ > >> > Bioc-sig-sequencing mailing list > >> > [email protected] > >> > <mailto:[email protected]> > >> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > >> > > >> > > >> > _______________________________________________ > >> > Bioc-sig-sequencing mailing list > >> > [email protected] > >> > <mailto:[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 > > > > > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
