rscharpf/oligoClasses — Issue #1: Annotation packages for marker-level classes to include 'universe' or 'genomeBuild' slot?
Author: rscharpf
Created: 2012-02-02 13:50:40+00:00
State: open

I have defined most of the marker-level classes in oligoClasses (e.g., oligoSnpSet) to use GenomeAnnotatedDataFrame for the featureData slot.

E.g.,

setClass("oligoSnpSet", contains="SnpSet",
representation(featureData="GenomeAnnotatedDataFrame")) ## total copy number and genotypes

The rational is that most people will want the genomic annotation for the markers and AnnotatedDataFrame does not ensure that the columns have a uniform labeling and does not enforce the class of the vectors. For example, chromosome could be an integer or a character string. GenomeAnnotatedDataFrame provides a standard label and requires that 'chromosome' is an integer. The effort for adding this information should be fairly minimal -- I've created GenomeAnnotatedDataFrameFrom methods (just like AnnotatedDataFrameFrom in Biobase) to make this more or less automatic.

A 'wish list' for me is the ability to also specify the build to use when annotating the markers -- e.g, hg18 or hg19 -- through a universe argument. This would be easily done using the *Crlmm annotation packages by adding the extension 'hg18' and 'hg19' to the R objects saved in inst/extdata. For the pd.* packages, I think it would be fine to just have the latest build as having both would make these packages too big.

Would appreciate comments regarding this. If this seems sensible, I think we should also have a 'genomeBuild' or 'universe' slot in the marker-level classes...