On 3/19/09, Martin Morgan <[email protected]> wrote: > Hi Ivan --
[...] > chipseq is in the devel branch, and data structures there have not > been fully aligned with other established structures, and vice versa, > and the chipseq data structures are not fully described. This is a > disconnect that we're working to resolve before the release. > > Others might have something else to say. You'll find these scripts more current: http://www.bioconductor.org/workshops/2009/SeattleJan09/ChIP-seq/ The use of "AlignedList" has been superceded by the "GenomeData" and "GenomeDataList" classes defined in the BSgenome package. You can convert an "AlignedRead" object to a "GenomeData" object by as(obj, "GenomeData") (which basically strips off everything except alignment location). To work with a list of "GenomeData" objects (e.g. different lanes), see ?GenomeDataList. -Deepayan _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
