[BioC] How to get closest gene around chromosome location?[biomaRt]

[Sean Davis]

On Tue, Oct 28, 2008 at 4:57 AM, João Fadista <Joao.Fadista at agrsci.dk> wrote:
>
> Hi Sean,
>
> Concerning the getRefflat function, I can´t seem to get it to work with bos taurus nor human. Is it because I am having R version 2.6.0?
>
>> rf <- getRefflat('bosTau4')
> trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/bosTau4/database/refFlat.txt.gz'
> Content type 'application/x-gzip' length 906439 bytes (885 Kb)
> opened URL
> downloaded 885 Kb
>
> Error in pushBack(c(lines, lines), file) :
>  can only push back on text-mode connections

Hi, Joao.

ACME_1.8.0 is meant to be used with R-2.8.0.  It looks like ACME_1.4.0
is appropriate for R-2.6.0 and it passes on the build report for
R-2.6.0 on Windows.

Sean

>> sessionInfo()
> R version 2.6.0 (2007-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] ACME_1.8.0
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean Davis
> Sent: Monday, October 27, 2008 7:24 PM
> To: Hooiveld, Guido
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] How to get closest gene around chromosome location?[biomaRt]
>
> On Mon, Oct 27, 2008 at 12:45 PM, Hooiveld, Guido <Guido.Hooiveld at wur.nl> wrote:
>>
>> Dear list,
>> Anyone a pointer / piece of code on how to find genes that are closest
>> to a specific chromosomal location?
>>
>> I am using Biostrings and associated mouse genome package to find and
>> localize specific sequences (putative TFBS). This works fine (thanks
>> Herve for the clear vignette). I have now an output (list) like this:
>>
>> seqname start  end  strand patternID
>> chr1 7196884  7196895  +  GH_TEST
>> chr1 15433465 15433476 +  GH_TEST
>> chr1 78251474 78251485 +  GH_TEST
>> chr1 82635484 82635495 +  GH_TEST
>> chr1 22603411 22603422 -  GH_TEST
>> chr1 34167820 34167831 -  GH_TEST
>> chr1 47227452 47227463 -  GH_TEST
>>
>> Next I would like to know which gene is closest to the each entry, and
>> what the distance is.
>> For example, info like the first entry is situated 1234 bp upstream of
>> the TSS of gene ENSMUSG000xx, and entry 2 is located 3456 bp
>> downstream of the TSS of gene ENSMUSG00yy. Etc.
>>
>> I am thinking of using BiomaRt for this, but I don't know how to do
>> this.
>>
>> Note: In the archive I did find a related thread but the functions
>> given unfortunately do not give the info I am after.
>> http://article.gmane.org/gmane.science.biology.informatics.conductor/5
>> 09
>> 7
>>
>> Any suggestions are appreciated,
>
> The findClosestGene() function in the ACME package will do this using RefSeq data from UCSC.
>
> Sean
>
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