Hi Harris,

With a small number of regions:
> re2genestest <-
bumphunter::matchGenes(x=regr[1:2],build='hg19',promoterDist=5000,all=TRUE,
mc.cores=1, verbose=TRUE)
Matching regions to genes.
nearestgene: loading bumphunter hg19 transcript database
finding nearest transcripts...
AnnotatingDone.
> head(re2genestest)
queries         Tx   name annotation
      1 uc009vis.3 WASH7P  NR_024540
      1 uc009vit.3 WASH7P  NR_024540
      1 uc009viu.3 WASH7P  NR_024540
      1 uc001aae.4 WASH7P  NR_024540
      1 uc001aah.4 WASH7P  NR_024540
      1 uc009vir.3 WASH7P  NR_024540


With a high number of regions:
> re2genestest <-
bumphunter::matchGenes(x=regr[1:10000],build='hg19',promoterDist=5000,all=TRUE,
mc.cores=1, verbose=TRUE)
Matching regions to genes.
nearestgene: loading bumphunter hg19 transcript database
finding nearest transcripts...
Splitting the annotation into 3 chunks of 10000 regions each
Annotating..........Done.
Annotating..........Done.
Annotating.Done.
> head(re2genestest)
    name annotation description
1 WASH7P  NR_024540        <NA>
2 WASH7P  NR_024540        <NA>
3 WASH7P  NR_024540        <NA>
4 WASH7P  NR_024540        <NA>
5 WASH7P  NR_024540        <NA>
6 WASH7P  NR_024540        <NA>

I can bypass the bug by splitting my regions into a list of 3000 regions at
each iteration and then using rbind on the output data.frames.

Best,
Anne




On Fri, Jul 26, 2013 at 8:14 AM, Harris A. Jaffee <hj@jhu.edu> wrote:

> 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@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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>

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