Hi there, I have a suggestion - is it possible to make it a little easier to directly calculate weighted coverage on a GRanges object that has regions on >1 chromosome? I think the code below explains what I mean.
I've figured out a workaround, but it took me quite a while to get there - perhaps putting the coercion in the underlying coverage/weights code will help others avoid that in future? thanks very much, Janet ------------------------------------------------------------------- Dr. Janet Young (Trask lab) Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., C3-168, P.O. Box 19024, Seattle, WA 98109-1024, USA. tel: (206) 667 1471 fax: (206) 667 6524 email: jayoung ...at... fhcrc.org http://www.fhcrc.org/labs/trask/ ------------------------------------------------------------------- library(GenomicRanges) dat1 <- GRanges(seqnames="chr2L",IRanges(start=((1:4)*5),width=20),score=c(3,5,10,20) ) dat2 <- GRanges(seqnames=rep(c("chr2L","chr3L"),c(4,3)),IRanges(start=c( (1:4)*5 , (1:3)*5 ),width=20),score=c(3,5,10,20,6,10,30) ) seqlengths(dat2) <- c(50,40) #### this works coverage(dat1,weight=list(elementMetadata(dat1)$score)) ## SimpleRleList of length 1 ## $chr2L ## 'integer' Rle of length 39 with 8 runs ## Lengths: 4 5 5 5 5 5 5 5 ## Values : 0 3 8 18 38 35 30 20 #### this works myscores <- list(c(3,5,10,20), c(6,10,30)) coverage(dat2,weight=myscores) ## SimpleRleList of length 2 ## $chr2L ## 'integer' Rle of length 50 with 9 runs ## Lengths: 4 5 5 5 5 5 5 5 11 ## Values : 0 3 8 18 38 35 30 20 0 ## $chr3L ## 'integer' Rle of length 40 with 7 runs ## Lengths: 4 5 5 10 5 5 6 ## Values : 0 6 16 46 40 30 0 ##### but it'd be great if this could work too.... coverage(dat2,weight=list(elementMetadata(dat2)$score)) ## Error in normargWeight(weight, nseq) : 'weight' is longer than 'x' ### for now I'll coerce my scores into a list by chromosome: does this seem to be a reliable way to do it? this is the part it took me a while to figure out on my own... myscores <- split( elementMetadata(dat2)$score , as.character(seqnames(dat2)) ) coverage(dat2,weight=myscores) 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_1.4.3 IRanges_1.10.0 _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
