Is this being taken into consideration by anyone? Will it be worked on?
Thanks,
Michael
On Thu, Dec 12, 2013 at 1:36 PM, Michael Lawrence <micha...@gene.com> wrote:
> We've found that analysts often need to restrict seqlevels to certain
> pre-defined sets of chromsomes. Given the variability across organisms, it
> would be nice to have an abstraction.
>
> We often see this in code:
>
> keepSeqlevels(seqinfo, as.character(1:22)
> keepSeqlevels(seqinfo, c(1:22, "X", "Y"))
>
> Perhaps instead we could the more abstract and arguably more readable:
>
> keepAutosomes(seqinfo)
> keepPrimaryChromosomes(seqinfo)
>
> Not sure of the best term for the latter. It refers to the set of
> chromosomes that are not assembly fragments but are generally in the
> nucleus (when there is one).
>
> It would also be nice to have a sort,Seqinfo method that sorts by the
> natural ordering of the chromosomes, if there is one. Maybe the function
> needs its own name, but either way, this is something that really needs to
> be in the infrastructure.
>
> I think the existing SeqnameStyle infrastructure should be able to support
> this.
>
> Thoughts?
>
> Michael
>
>
>
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