[BioC] biomaRt: using a list as values. confused...

[J.delasHeras at ed.ac.uk]

Hi Stephen,

many thanks for that. I was looking at the previous results that I  
said were ok and realised the ranges were wrong and that confused me  
even more!

Thanks for teh tip about the chromosomal region, that's just what I needed!

Jose


Quoting Steffen Durinck <durinck.steffen at gene.com> on Thu, 9 Jun 2011  
09:12:59 -0700:

> Hi Jose,
>
> the combo filter chr + start + end is a special situation and is
> interpreted as give me everything in between.  It is porbably not well
> documented but this however filter combo works only for a single
> region at a time so your second example is correct there are only few
> genes in your region on chr1.
>
> An alternative which does work for multiple regions is to use the
> chromosomal_region filter like:
>
> regions<-c("1:11401198:11694590", "2:86460656:86663869")
> attributes<-c("hgnc_symbol", "entrezgene",
> "chromosome_name","start_position", "end_position", "strand", "band")
> getBM(attributes=attributes,filters="chromosomal_region",values=regions,mart=ensembl)
>
> Cheers,
> Steffen
>
> On Thu, Jun 9, 2011 at 8:49 AM,  <J.delasHeras at ed.ac.uk> wrote:
>>
>> I'm trying to obtain information about genes within a number of regions
>> defined by a chromosome name, start and end coordinates.
>>
>> I understand that the way to specify multiple filters to be used together (a
>> set of chr+start+end) is to use a list for 'values'.
>>
>> This seems to work ok when I have more than one region (I tested it using
>> two regions first, before doing the proper search for >1000), but if I were
>> to specify just one region, it does not work... and I'm wondering how I
>> would do it in that case.
>>
>> Example:
>>
>> library("biomaRt")
>> ensembl = useMart("ENSEMBL_MART_ENSEMBL",
>>   dataset="hsapiens_gene_ensembl",
>>   host="www.ensembl.org")
>>
>> chrom<-c("1", "2")
>> chr.start<-c(11401198, 86460656)
>> chr.stop<-c(11694590, 86663869)
>>
>> attributes<-c("hgnc_symbol", "entrezgene", "chromosome_name",
>> "start_position", "end_position", "strand", "band")
>>
>>
>> # extract both regions at once:
>> getBM(attributes=attributes,
>>      filters=c("chromosome_name","start","end"),
>>      values=list(chrom,chr.start,chr.stop),mart=ensembl)
>> #this works, returning 1939 rows of data, the first 1198 with chr1
>> #corresponding to teh first region, and the rest with chr2 to teh second.
>> Good.
>>
>> #but how does one retrieve the data for just ONE region?
>> # try this:
>> getBM(attributes=attributes,
>>      filters=c("chromosome_name","start","end"),
>>      values=list(chrom[1],chr.start[1],chr.stop[1]),mart=ensembl)
>> # it only returns one gene!!! (in two rows)
>>
>> so, when I just want to do a single search with multiple filters, how would
>> I specify the values?
>>
>> Jose
>>
>> --
>> Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
>> The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6507090
>> Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
>> Swann Building, Mayfield Road
>> University of Edinburgh
>> Edinburgh EH9 3JR
>> UK
>>
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
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>>
>
>



-- 
Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6507090
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.