On 06/22/2011 05:33 PM, Janet Young wrote:
Hi again,Thanks, Michael - looking forward to seqselect on GRanges being implemented, if possible. Getting a little further through my old code, brings up another related request. Here are some slightly different example ranges: myGR<- GRanges(seqnames=c("chr1","chr2","chr2"),ranges=IRanges(start=c(25,40,60),end=c(35,45,65)) ) myRD<- RangedData(space=c("chr1","chr2","chr2"),IRanges(start=c(25,40,60),end=c(35,45,65)) ) And I had previously been using this command: restrict(ranges(myRD), 30,50) I'm doing that because I'm interested in ranges within the same region on every single "chromosome". With my real data, they spaces/seqnames are not chromosomes, they're promoter regions centered around the transcription start site, and I want to take various equivalent sub-portions of the whole set of promoters) I can't get "restrict" to work on the GRanges object at the moment (even if I try that same coercion first): restrict( myGR , 30,50) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "restrict", for signature "GRanges" restrict( as(myGR,"RangesList") , 30,50) Error in sapply(listData, function(Xi) extends(class(Xi), elementTypeX)) : error in evaluating the argument 'X' in selecting a method for function 'sapply': Error in .CompressedList.list.subscript(X = X, INDEX = seq_len(length(X)), : invalid output element of class "IRanges" It would be great if restrict could work directly in the same way as it did for RangedData. In the meantime I can probably figure out a way to do it with lapply.
or rng <- restrict(ranges(gr), 30, 50, keep.all.ranges=TRUE) ranges(gr) <- rng gr[width(gr) != 0] (and similarly for GRangesList). Martin
thanks, Janet On Jun 22, 2011, at 4:19 PM, Michael Lawrence wrote:Hi, There is already a coercion from GRanges to RangesList, i.e., as(gr, "RangesList"). That said, seqselect() should have a method for GRanges, if possible. Michael On Wed, Jun 22, 2011 at 4:15 PM, Janet Young<jayo...@fhcrc.org> wrote: Hi again, A further note - the workaround I first emailed only works when there's one range per chromosome. I have a better workaround now - the coercion looks like this instead: convertGRangesToCompressedIRangesList<- function (myGRobject) { myGR_convert<- split(myGRobject, seqnames(myGRobject) ) names(myGR_convert)<- unlist(lapply(myGR_convert, function(x) { as.character(seqnames(x))[1] })) myGR_convert<- lapply(myGR_convert, ranges ) class(myGR_convert)<- "CompressedIRangesList" myGR_convert } Janet Begin forwarded message:From: Janet Young<jayo...@fhcrc.org> Date: June 22, 2011 4:01:03 PM PDT To: Bioc-sig-sequencing@r-project.org Subject: seqselect using GRanges object on multiple chromosomes Hi there, I'm updating some of my older code - I was previously storing regions of interest as RangedData but now I'm switching to GRanges. I'm running into a little trouble with seqselect - I've found a workaround but wanted to suggest extending seqselect so it can work with GRanges objects directly. I have some scores for each base-pair I've stored as a SimpleRleList object. I want to use GRanges object with seqselect to pull out scores from my regions of interest, but to make that work I first have to do an odd (and slightly wrong-looking, to me) coercion of my GRanges object to a CompressedIRangesList. I think the code below explains all (?). thanks very much, Janetlibrary(GenomicRanges)Loading required package: IRanges Attaching package: 'IRanges' The following object(s) are masked from 'package:base': cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union### make some scores objects, for single chromosomes, or across several chrs tempscores<- Rle(1:20) tempscores2<- Rle(101:120) allscores<- RleList(chr1=tempscores,chr2=tempscores2) # yields a SimpleRleList ## make some ranges objects myIR<- IRanges(start=3,end=5) myGR<- GRanges(seqnames=c("chr1","chr2"),ranges=IRanges(start=3,end=5)) myRD<- RangedData(space=c("chr1","chr2"),IRanges(start=c(3,3),end=c(5,5)) ) ### test seqselect: seqselect(tempscores,myIR) #works'integer' Rle of length 3 with 3 runs Lengths: 1 1 1 Values : 3 4 5seqselect(allscores,myGR) # doesn't workError in seqselect(allscores, myGR) : unrecognized 'start' typeseqselect(allscores,myRD) # doesn't workError in seqselect(allscores, myRD) : unrecognized 'start' typeseqselect(allscores,ranges(myRD)) # works. ranges(myRD) is a CompressedIRangesListSimpleRleList of length 2 $chr1 'integer' Rle of length 3 with 3 runs Lengths: 1 1 1 Values : 3 4 5 $chr2 'integer' Rle of length 3 with 3 runs Lengths: 1 1 1 Values : 103 104 105seqselect(allscores,ranges(myGR)) # doesn't workError in .bracket.Index(start, length(x), names(x), asRanges = TRUE) : range index out of boundsseqselect(allscores,split(myGR)) # doesn't workError in seqselect(allscores, split(myGR)) : unrecognized 'start' type#### coerce myGR to something that looks a bit like a CompressedIRangesList myGR_convert<- split(myGR) names(myGR_convert)<- names(seqlengths(myGR_convert)) myGR_convert<- lapply(myGR_convert, ranges ) class(myGR_convert)<- "CompressedIRangesList" seqselect(allscores,myGR_convert) # worksSimpleRleList of length 2 $chr1 'integer' Rle of length 3 with 3 runs Lengths: 1 1 1 Values : 3 4 5 $chr2 'integer' Rle of length 3 with 3 runs Lengths: 1 1 1 Values : 103 104 105sessionInfo()R version 2.13.0 (2011-04-13) Platform: i386-apple-darwin9.8.0/i386 (32-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] GenomicRanges_1.4.6 IRanges_1.10.4_______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing_______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
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