I forgot: > 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] stats graphics grDevices utils datasets methods base other attached packages: [1] chipseq_0.1.11 ShortRead_1.1.43 lattice_0.17-20 BSgenome_1.11.13 [5] Biostrings_2.11.40 IRanges_1.1.48 loaded via a namespace (and not attached): [1] Biobase_2.3.10 grid_2.9.0 hwriter_1.1 ________________________________ From: Michael Lawrence <[email protected]> Cc: [email protected] Sent: Monday, 20 April, 2009 15:00:01 Subject: Re: [Bioc-sig-seq] A myriad of classes 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
