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
