Michael Lawrence wrote: > On Mon, Oct 19, 2009 at 10:25 AM, Chris Seidel <[email protected]> wrote: > >> In using gdapply to get coverage over all chromosomes of a >> GenomeDataList object: >> >> cov <- gdapply(extendedReads, coverage)
a different route to this point (<...> representing arguments you'd provide) is aln <- readAligned(<...>) # or aln <- AlignedRead(<...>) library(BSgenome.Hsapiens.UCSC.hg18) wd <- seqlengths(Hsapiens) ## subset aln and wd so that they have matching names, e.g., ## it might also be necessary to adjust names, e.g,. dropping '.fa' aln <- aln[chromosome(aln) %in% names(wd)] wd <- wd[names(wd) %in% chromosome(aln)] cvg <- coverage(aln, width=wd, extend=200L) this also results in a list of Rle's (a SimpleRleList). See ?"AlignedRead-class" for details; this is a non-trivial operation, e.g., it maybe useful to separately manage strands. Martin >> >> how do you supply the "width" argument to coverage? When I try handing >> it a vector of chromosome lengths, it complains that it needs a single >> value. >> >> > This is the normal behavior of apply functions in R. The additional > arguments are passed in whole to the function every time it is invoked. We > don't have an "mapply" variant of gdapply, so you'll need to do some extra > work, like keeping track of an index. > > Perhaps we could make this easier using metadata? We know the genome of > 'extendedReads' so 'coverage' could be smart and refer to the appropriate > BSgenome package. > > Michael > > > >> -Chris >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
