Hi Michael,
On 07/24/2014 10:24 AM, Michael Lawrence wrote:
Seems like this should work genome(gene.models) <- "GRCh37" but Error in .seqinfo.TranscriptDbReplace(x, new2old = new2old, force = force, : 'new2old' must be specified when replacing the 'seqinfo' of a TranscriptDb object
The error message doesn't help but the only thing in a TranscriptDb object that can be modified is the seqlevels. Since TranscriptDb objects are essentially read-only, this is achieved by storing the user-supplied seqlevels in a slot. Supporting user-supplied seqlengths, circularity flags and genome is doable but would require modifying the definition of the TranscriptDb class first. I'm adding this to our list. BTW, everybody seems to be using TxDb as an abbreviation for TranscriptDb these days. I guess this is because we also have the TxDb.* packages which are just TranscriptDb objects wrapped into packages. So I guess it's time to rename the TranscriptDb class -> TxDb. Cheers, H.
Michael [[alternative HTML version deleted]]
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