On Mon, Mar 23, 2009 at 11:18 AM, <[email protected]> wrote: > > Hello Deepayan and all, > > I think that I understood well but the conversion does not work. This is a > copy paste of the session: > > library(ShortRead) > Loading required package: IRanges > > Attaching package: 'IRanges' > > > The following object(s) are masked from package:base : > > cbind, > duplicated, > order, > pmax, > pmax.int, > pmin, > pmin.int, > rank, > rbind, > rep.int, > sapply, > sort, > table, > unique > > Loading required package: Biostrings > Loading required package: BSgenome > Loading required package: lattice > setwd('/scratch1/igregore/ChIPseq/runs/09-03-03/GERALD_16-03-2009_niddk/') > pattern <- "s_7_export.txt" > filt1 <- alignDataFilter(expression(filtering == "Y")) > filt2 <- chromosomeFilter("chr1.fa") > filt <- compose(filt1, filt2) > aln_chr1 <- readAligned(".", pattern, "SolexaExport", filter = filt) > class(aln_chr1) > [1] "AlignedRead" > attr(,"package") > [1] "ShortRead" > alignedLocs <- as(aln_chr1, "GenomicData")
Try alignedLocs <- as(aln_chr1, "GenomeData") (sorry for the confusing names, but somewhat inevitable for a devel package). -Deepayan _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
