Hi, On Tue, May 24, 2011 at 11:34 AM, Fabrice Tourre <fabrice.ciup at="" gmail.com=""> wrote: > Steve, > > It make sense. > > Thank you very much. Nice -- one last thing. If you will be taking the Views route, read through this recent thread from the bioc-sig-seq mailing list: https://stat.ethz.ch/pipermail/bioc-sig- sequencing/2011-May/001985.html In particular this (very detailed) explanation from Herve about when/how you might want to use compact with Views so that you don't end up trying to store your entire genome in RAM: https://stat.ethz.ch/pipermail/bioc-sig- sequencing/2011-May/002000.html Hope that helps, -steve > > On Tue, May 24, 2011 at 5:19 PM, Steve Lianoglou > <mailinglist.honeypot at="" gmail.com=""> wrote: >> Hi, >> >> On Tue, May 24, 2011 at 9:18 AM, James W. MacDonald >> <jmacdon at="" med.umich.edu=""> wrote: >>> Hi Fabrice, >>> >>> On 5/24/2011 4:56 AM, Fabrice Tourre wrote: >>>> >>>> Dear list, >>>> >>>> How can I get all 3'utr and 5'utr region from GenomicFeatures of Human? >>>> There are fiveUTRsByTranscript, threeUTRsByTranscript methods in >>>> GenomicFeatures. But how can I get these regions? >>> >>> hg19 <- makeFeatureDbFromUCSC(genome = "hg19", table = "refGene") >>> utr3 <- threeUTRsByTranscript(ref19) >>> >>> Which seems pretty obvious to me, given the help pages for these functions. >>> >>> It would be helpful if you could give us an indication of where you got >>> stuck, and what in particular you didn't understand from the help pages, so >>> we can improve our documentation. >> >> Perhaps the OP wanted to know how to get the sequences from those >> regions, given the results from those functions? >> >> If that's the case, I'd load up the BSgenome.Hsapiens.UCSC.hg19 >> library, iterate over my results one chromosome at a time, and use a >> mix of the Views function over the unmasked chromosome (using ranges >> across the 3'utr across the chromosome as the second argument) ... >> you'll have to take care of seqs on the reverse strand. >> >> You could also look at the getSeq function. >> >> I'lll leave the actual writing of the code as an exercise to the >> reader since I think it's useful to know how Views work and you'll >> have to read up on the documentation a bit :-) >> >> -steve >> >> -- >> Steve Lianoglou >> Graduate Student: Computational Systems Biology >> ?| Memorial Sloan-Kettering Cancer Center >> ?| Weill Medical College of Cornell University >> Contact Info: http://cbio.mskcc.org/~lianos/contact >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact