On Mon, Apr 20, 2009 at 11:19 AM, <[email protected]> wrote: > > Hello fellow listers, > > Is there a document summarizing the myriad of data containing classes? >
No, not yet. We're working on a vignette for the IRanges package (we'll have something in about a week), which will need to be complemented by additional vignettes in Biostrings and BSgenome. There is probably also a need for a high-level vignette explaining the sequence infrastructure in BioC. > > I am trying to find a map to help me understand what is the difference > between, say, GenomicData, GenomeData, GenomedataList, etc. > > I need to be able to inter-convert data, merge different sources of data, > and also subset data. > Can you be more specific? GenomicData is no longer a class, but there is a GenomicData function, which is a genome-oriented constructor for RangedData in the rtracklayer package. GenomeData (from the BSgenome package) is for storing arbitrary data objects on a per chromosome level. RangedData (in IRanges) is similar, except the data need to fit into a rectangular data.frame-like structure. Hope this helps and sorry for the confusion, Michael > > For a single class, I think that finding the information is easy. For many > classes, it gets challenging. > > A possible solution is reading the whole BioC documentation but then BioC > rises a productivity issue for users that are not developers. > > Anybody can advice? > > Thank you, > > Ivan > > > > > _______________________________________________ > 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
