Dear BSgenome developers,

I would like to change the seqnames of a loaded BSgenome package and wonder if it is possible.

But I find that the the seqinfo of a BSgenome is not updateable, instead raising the error

unable to find an inherited method for function "seqinfo<-", for signature "BSgenome"

This happens when I try either to directly update the seqnames, or I try to set the seqinfo to one so crafted.

Is there some workaround for this and/or could the BSgenome seqinfo be allowed to be updateable?

Perhaps there an easy way to 'forge' a new BSgenome as a clone of another, only with the seqnames re-set ...???

I am constantly mapping between UCSC-style chromosome names (such as 'chr2L', 'chrM' etc) and Flybase (such as '2L', 'dmel_mitochondrion_genome', etc) and would  find it very useful to have a parallel BSgenome to "BSgenome.Dmelanogaster.UCSC.dm3" with the chromosome's so re-named.

Perhaps there is a different best practice I should adopt.  All suggestions welcome!

Thanks,

Malcolm Cook
Stowers Institute for Medical Research


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