Dear Benjamin,
Thank you for pointing out the typo. We will fix it in ensembl mart 72
scheduled for June 2013.
Regards,
Thomas
On 26 May 2013, at 17:34, Benjamin Dubreuil wrote:
> Hi,
>
> But I noticed a typo with the human attributes name.
>
> >library(biomaRt)
> >human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> > listAttributes(human)[624,]
> name
> description
> 624 mdomestica_homology_ensembl_gene Opossum Ensembl
> Gene ID
>
> > listAttributes(human)[590,]
> name
> description
> 590 mmusculus_homolog_ensembl_gene Mouse Ensembl
> Gene ID
>
>
> The attribute name "mdomestica_homology_ensembl_gene" should be replaced by
> "mdomestica_homolog_ensembl_gene".
>
> Best.
>
> Benjamin Dubreuil
>
> Date: Thu, 23 May 2013 11:42:27 -0700
> Subject: Re: [BioC] [biomaRt] Finding Orthologs genes between Human and Mouse
> - problem with getBM to retrieve some attributes
> From: [email protected]
> To: [email protected]
> CC: [email protected]
>
> Hi Benjamin,
> I provided a work around to your question on the biomart user list but will
> repost this on the bioc list:
> The problem is on the R side, matching the BioMart header info back up with
> the attribute name for the mmusculus_homolog_perc_id attribute. 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
>
> Cheers,
> Steffen
>
> On Wed, May 22, 2013 at 7:49 AM, Benjamin Dubreuil
> <[email protected]> wrote:
> Hi folks,
>
> I'm having a problem with getBM function from biomaRt package.
> 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
>
> [[alternative HTML version deleted]]
>
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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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