[BioC] transcriptsBy via TxDb.Hsapiens.UCSC.hg19.knownGene painfully slow

[Martin Morgan]

On 01/01/2013 01:32 PM, Murat Tasan wrote:
> hi all - does anyone have any performance tips for using
> transcriptsBy(TXDB, by = "gene") with the UCSC transcript database?
> in particular, is the SQLite backing database file indexed (along columns
> holding the internal IDs)?
> i'd provide some timing results for the command execution, but i ran out of
> patience after about 10 minutes with no results...

it is 'slow' but only in the couple of seconds definition of slow. Something 
else is going on so a reproducible example, including sessionInfo(), would be 
helfpul.


>
> cheers,
>
> -m
>
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