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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