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. 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, > > > > Janet > > > > > > > > > > > >> library(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 5 > >> seqselect(allscores,myGR) # doesn't work > > Error in seqselect(allscores, myGR) : unrecognized 'start' type > >> seqselect(allscores,myRD) # doesn't work > > Error in seqselect(allscores, myRD) : unrecognized 'start' type > >> > >> seqselect(allscores,ranges(myRD)) # works. ranges(myRD) is a > >> CompressedIRangesList > > SimpleRleList 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 : 103 104 105 > > > >> > >> seqselect(allscores,ranges(myGR)) # doesn't work > > Error in .bracket.Index(start, length(x), names(x), asRanges = TRUE) : > > range index out of bounds > >> seqselect(allscores,split(myGR)) # doesn't work > > Error 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) # works > > SimpleRleList 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 : 103 104 105 > > > >> > >> sessionInfo() > > 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