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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