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