[Bioc-devel] changing genome of TxDb

Hervé Pagès hpages at fhcrc.org
Fri Jul 25 20:48:15 CEST 2014

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

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.


> Michael
> 	[[alternative HTML version deleted]]
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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