Hi Thomas, Benjamin,
The problem is on the R side, the "%" symbol in the attributes names (%
Identity with respect to query gene) are causing trouble, I am working on a
fix. Until then you can add bmHeader=FALSE to your getBM query and things
should work (see below):
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> attributes =
c("ensembl_gene_id","mmusculus_homolog_ensembl_gene","mmusculus_homolog_perc_id_r1")
> attributes=c(attributes,"mmusculus_homolog_orthology_type",
"mmusculus_homolog_subtype", "mmusculus_homolog_perc_id")
> orth.mouse = getBM( attributes,filters="with_homolog_mmus",values =TRUE,
mart = human, bmHeader=FALSE)
> dim(orth.mouse)
[1] 22886 6
Best,
Steffen
On Wed, May 22, 2013 at 7:05 AM, Thomas Maurel <[email protected]> wrote:
> Dear Benjamin,
>
> I can't see what's wrong with your query, but it looks like the issue is
> coming from the following attributes:
> "mmusculus_homolog_orthology_type"
> "mmusculus_homolog_subtype"
> "mmusculus_homolog_perc_id"
>
> If you do the following query you will get the same error back:
>
> > library(biomaRt)
> > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> > attributes =
> c("ensembl_gene_id","mmusculus_homolog_ensembl_gene","mmusculus_homolog_orthology_type")
> > orth.mouse = getBM(attributes, filters="with_homolog_mmus",values=TRUE,
> mart = human, uniqueRows=TRUE)this might be a bug coming from the biomaRt
> package. I would advise you to email the bioconductor list:
> [email protected]
> Error in `[.data.frame`(result, , attributes) :
> undefined columns selected
>
> It's when you start adding one of the previous attribute that the query
> fail.
> I have also try your query with the host pointing to ensembl.org and I am
> getting the same error.
> Since the query is working fine on the biomart interface, this might be a
> bug coming from the biomaRt package. I would advise you to email the
> bioconductor list: [email protected]
>
> Hope this helps,
> Regards,
> Thomas
> On 22 May 2013, at 09:47, Benjamin Dubreuil wrote:
>
> Hi folks,
>
> I'm having a problem with getBM function.
> I would like to retrieve the orthologs genes between Human and Mouse, with
> their percentage of identity to one another, their orthology relationship
> and their common ancestor.
>
> I did this, and it works fine :
>
> >library(biomaRt)
> >human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> >attributes =
> c("ensembl_gene_id","mmusculus_homolog_ensembl_gene","mmusculus_homolog_perc_id_r1")
> > orth.mouse = getBM(attributes, filters="with_homolog_mmus",values=TRUE,
> mart = human, uniqueRows=TRUE)
> > dim(orth.mouse)
> [1] 22886 3
> >
>
> But when I'm adding some attributes, I get an error :
>
> >attributes=c(attributes,"mmusculus_homolog_orthology_type",
> "mmusculus_homolog_subtype", "mmusculus_homolog_perc_id")
> > orth.mouse = getBM( attributes,filters="with_homolog_mmus",values =TRUE,
> mart = human)
> Error in `[.data.frame`(result, , attributes) :
> undefined columns selected
>
>
> I've checked the attributes names, I didnt make any typos:
> > listAttributes(human)[c(1,567,573:576),]
> * name
> description*
> 1 ensembl_gene_id
> Ensembl Gene ID
> 567 mmusculus_homolog_ensembl_gene Mouse Ensembl
> Gene ID
> 573 mmusculus_homolog_orthology_type Homology Type
> 574 mmusculus_homolog_subtype Ancestor
> 575 mmusculus_homolog_perc_id %
> Identity with respect to query gene
> 576 mmusculus_homolog_perc_id_r1 % Identity
> with respect to Mouse gene
>
> Can anyone see what I'm doing wrong ?
>
>
> Best.
>
> Dubreuil Benjamin
> E. Levy Group (The Cell architecture Lab)
> Weitzmann Insitute of Science, ISRAEL
> Kimmelman Building, 4th floor, room 410
> _______________________________________________
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>
>
> --
> Thomas Maurel
> Bioinformatician - Ensembl Production Team
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
>
>
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