[BioC] bumphunter::matchGenes and all=TRUE

[Harris A. Jaffee]

Anne,

Can you run it with 'verbose=TRUE'?  Also, tell us what your mc.cores
value is (This will also appear in the verbose output.)?  If it's >1,
please try 'mc.cores=1' to see if that makes any difference.

On Jul 26, 2013, at 9:45 AM, Kasper Daniel Hansen wrote:

> This sounds weird and it sounds like a bug.  We'll have a look.
> 
> You can (greatly) speed up the process by providing some example object(s)
> and code to show the error.
> 
> Best,
> Kasper
> 
> 
> On Thu, Jul 25, 2013 at 8:13 PM, Anne Biton <anne.biton at berkeley.edu> wrote:
> 
>> Hello,
>> 
>> I am using the function matchGenes of the package bumphunter to associate
>> many regions of interest with transcripts.
>> 
>> I use all=TRUE in order to get several results per region.
>> When I use all=TRUE and a small amount of queries, the output indeed
>> contains the columns 'queries' and 'Tx' which give the query index and the
>> matching transcript.
>> But when I use all=TRUE and many regions (when the function starts to split
>> the data), the output data.frame does not contain anymore these two columns
>> and it is not possible to know which region is associated with which
>> transcript.
>> I think there is a problem in the function when the annotation is split
>> into chunks of 10000 regions each.
>> 
>> Please let me know if it can be solved!
>> 
>> Best regards,
>> Anne
>> 
>>        [[alternative HTML version deleted]]
>> 
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> 
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> 
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