Hi,
But I noticed a typo with the human attributes name.
>library(biomaRt)
>human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> listAttributes(human)[624,]
name
description624 mdomestica_homology_ensembl_gene
Opossum Ensembl Gene ID
> listAttributes(human)[590,] name
> description590
> 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
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