2011/8/11 Hervé Pagès <hpages@fhcrc.org> > Hi Michael, > > On 11-08-11 03:56 AM, Michael Lawrence wrote: > >> >> >> 2011/8/10 Hervé Pagès <hpages@fhcrc.org <mailto:hpages@fhcrc.org="">> >> >> >> Hi, >> >> Note that the "flank" method for GRanges objects is strand aware and >> in this context "end" means "3' end". If that's not what you want, >> just do something like >> >> start(grl) <- end(grl) + 1L >> end(grl) <- end(grl) + 10000L >> >> and you are done. >> >> But if you really want the "3' end", I can't think of an easy/efficient >> way, unless you do something *highly* NOT recommended like accessing >> directly a slot of your GRangesList object: >> >> <never do="" this!=""> >> >> grl@unlistData <- flank(grl@unlistData, 10000, start=FALSE) >> >> </never> >> >> Of course we should provide a "flank" method for GRangesList >> objects that will do the above so the user doesn't need to use >> a dangerous/forbidden trick ;-) >> >> >> >> It does sound from his variable names that he is looking for a >> strand-aware method, while the RangesList approach proposed by Martin is >> strand insensitive (but fairly efficient due to the compression). That >> is easy to fix though: >> >> ranges(grl) <- flank(ranges(grl), 10000, start = strand(grl) == "-") >> >> Having such a flank() would be great on GRangesList. >> >> Also, a simple unlist(grl, use.names=FALSE) and then resplitting is a >> way to avoid depending on any internals, without sacrificing too much >> performance. >> > > Yes, that's indeed cleaner. The resplitting can be a little bit tricky > though so I was thinking maybe we should have "relist" methods for > this. This would also allow to propagate all the metadata stuff (names, > metadata, elementMetadata) from the 'skeleton' arg: > > gr <- unlist(grl, use.names=FALSE) > gr2 <- FUN(gr) # FUN can be any isomorphism (i.e. endo > # that preserves the length) > grl2 <- relist(gr2, skeleton=grl) > > The relist part can be made really fast (as fast as the unlist part). > > I had actually already implemented an efficient relist(), but it is not yet exported, as I'm still testing it. A lot of this stuff I develop during an analysis and never get around to cleaning up. Michael > Cheers, > H. > > >> Michael >> >> >> H. >> >> >> >> On 11-08-10 02:48 PM, Martin Morgan wrote: >> >> On 08/10/2011 12:36 PM, Lakshmanan Iyer wrote: >> >> Hi, >> I am trying to add 10K to the end of the intervals in a >> GRangesList >> object using endoapply and flank using the comand: >> p3UTRs10K<- endoapply(p3UTRs,function (z) flank (z, >> 10000,start=FALSE)); >> >> >> maybe along the lines of >> >> example(GRangesList) >> ranges(grl) = flank(ranges(grl), 10000, start=FALSE) >> >> which gives >> >> > end(grl) >> CompressedIntegerList of length 3 >> [["gr1"]] 6 >> [["gr2"]] 9 15 >> [["gr3"]] 3 9 >> > ranges(grl) = flank(ranges(grl), 1000, start=FALSE) >> > start(grl) >> CompressedIntegerList of length 3 >> [["gr1"]] 7 >> [["gr2"]] 10 16 >> [["gr3"]] 4 10 >> > end(grl) >> CompressedIntegerList of length 3 >> [["gr1"]] 1006 >> [["gr2"]] 1009 1015 >> [["gr3"]] 1003 1009 >> >> ? Martin >> >> >> I am writing to find out if someone has a suggestion for a >> faster way >> of doing this? With 40000 elements it is taking a long time.. >> >> Here is what I am doing: >> >> class (p3UTRs) >> [1] "GRangesList" >> attr(,"package") >> [1] "GenomicRanges" >> >> length (p3UTRs) >> [1] 41053 >> >> p3UTRs10K<- endoapply(p3UTRs,function (z) flank (z, >> 10000,start=FALSE)); >> >> sessionInfo() >> >> R version 2.13.0 (2011-04-13) >> Platform: x86_64-apple-darwin9.8.0/x86__**_64 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/__**en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BSgenome.Mmusculus.UCSC.mm9_1.**__3.17 >> GenomicFeatures_1.4.0 >> [3] leeBamViews_0.99.11 BSgenome_1.20.0 >> [5] Biobase_2.12.1 Rsamtools_1.4.1 >> [7] Biostrings_2.20.0 GenomicRanges_1.4.3 >> [9] IRanges_1.10.0 rtracklayer_1.12.0 >> [11] RCurl_1.5-0 bitops_1.0-4.1 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.8.0 DBI_0.2-5 RSQLite_0.9-4 tools_2.13.0 >> XML_3.2-0 >> >> >> >> ______________________________**___________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**>> project.org <bioconductor@r-project.org>> >> >> https://stat.ethz.ch/mailman/_**_listinfo/bioconductor<h ttps:="" stat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >> <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor<ht="" tps:="" stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> > >> Search the archives: >> http://news.gmane.org/gmane.__**science.biology.informatics.__ >> **conductor<http: news.gmane.org="" gmane.__science.biology.informati="" cs.__conductor=""> >> <http: news.gmane.org="" gmane.**science.biology.informatics.**="">> conductor<http: news.gmane.org="" gmane.science.biology.informatics.c="" onductor=""> >> > >> >> >> >> >> >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M1-B514 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpages@fhcrc.org <mailto:hpages@fhcrc.org> >> Phone: (206) 667-5791 <tel:%28206%29%20667-5791> >> Fax: (206) 667-1319 <tel:%28206%29%20667-1319> >> >> >> ______________________________**___________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-**project.org<bioconductor@r-project.org> >> > >> >> https://stat.ethz.ch/mailman/_**_listinfo/bioconductor<https: s="" tat.ethz.ch="" mailman="" __listinfo="" bioconductor=""> >> <https: stat.ethz.ch="" mailman="" **listinfo="" bioconductor<https:="" st="" at.ethz.ch="" mailman="" listinfo="" bioconductor=""> >> > >> Search the archives: >> http://news.gmane.org/gmane.__**science.biology.informatics.__** >> conductor<http: news.gmane.org="" gmane.__science.biology.informatics="" .__conductor="">< >> http://news.gmane.org/gmane.**science.biology.informatics.**conduct or<http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> >> > >> >> >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M1-B514 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]