Hi, The GenomicData class does not exist right now. Please try as(cov, "RangedData").
Michael On Fri, Mar 13, 2009 at 9:08 AM, <[email protected]> wrote: > > Hello everybody, > > I am trying to somehow visualize how my reads overlap (or cover) mouse > chr1. A simple concept. > > I create a readAlign object like this > > aln <- readAlign(sp, myfile, filter = blah) > > fine. > > Then I compute the coverage like this > > cov <- coverage(aln, start=1)[[1]] > > fine. > > The problem arises when when I try to construct from the coverage: > > > gd <- as(cov, "GenomicData") > Error in as(cov, "GenomicData") : > no method or default for coercing "Rle" to "GenomicData" > > > So, basically, I am following Michael's tutorial > > http://www.bioconductor.org/workshops/2008/SeattleNov08/rtracklayer/rtracklayer.pdf > > Can anybody give me a pointer to figure out why it does not work for me? > > Thank you, > > Ivan > > > > > sessionInfo() > R version 2.9.0 Under development (unstable) (2009-03-10 r48103) > x86_64-unknown-linux-gnu > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] rtracklayer_1.3.9 RCurl_0.94-1 > [3] org.Mm.eg.db_2.2.6 RSQLite_0.7-1 > [5] DBI_0.2-4 AnnotationDbi_1.5.18 > [7] Biobase_2.3.10 BSgenome.Mmusculus.UCSC.mm9_1.3.11 > [9] ShortRead_1.1.43 lattice_0.17-20 > [11] BSgenome_1.11.13 Biostrings_2.11.40 > [13] IRanges_1.1.48 > > loaded via a namespace (and not attached): > [1] grid_2.9.0 hwriter_1.1 XML_2.3-0 > > > > > _______________________________________________ > 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
