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: durinck.steffen@gene.com > To: dubreuil.benjamin@hotmail.com > CC: bioconductor@r-project.org > > 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 <dubreuil.benjamin@hotmail.com> 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Users mailing list > Users@biomart.org > https://lists.biomart.org/mailman/listinfo/users -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge - CB10 1SD - UK [[alternative HTML version deleted]]