Hi,
With the convenience that seqnamesStyles offers now, having to specify
the chromosome name notation manually would feel like a step back. In
terms of subsetting genomic ranges, I normally think of four major
groups of interest:
- Toplevel/standard: 1,..22,X,Y,MT
- Autosomes: 1,..,22
- Allosomes: X,Y
- "Linear": 1,..,22,X,Y
If you are concerned about confusing the user with many specialized
functions, how about extending 'keepSeqlevels' by adding a e.g. 'group'
argument that allows you to select a group of chromosomes as above. As
an example, think of:
## subset as before by seqname
keepSeqlevels(gr, "1")
keepSeqlevels(gr, value = "1")
## the new feature
keepSeqlevels(gr, group = "autosomes")
which would dispatch to specialized methods like '.keepAutosomes' in
combination with 'seqnames.db'. This way, one could also create a
setting in which the groups can be easily extended by the user or other
packages, by simply defining more of the specialized functions.
Best wishes
Julian
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