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 <mflawren@fhcrc.org>

Cc: bioc-sig-sequencing@r-project.org
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




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