On Tue, Mar 16, 2010 at 5:25 PM, Jason Lu <jasonlu68@gmail.com> 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 <paboyoun@fhcrc.org>
> 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 <paboyoun@fhcrc.org>
> 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 <paboyoun@fhcrc.org
> >> > <mailto:paboyoun@fhcrc.org>> 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
> >> >         Bioc-sig-sequencing@r-project.org
> >> >         <mailto:Bioc-sig-sequencing@r-project.org>
> >> >         https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >> >
> >> >
> >> >     _______________________________________________
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> >> >     <mailto:Bioc-sig-sequencing@r-project.org>
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> >> >
> >> >
> >>
> >>
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> >>
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> >
>

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