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Question: [biomaRt] Finding Orthologs genes between Human and Mouse - problem with getBM to retrieve some attributes
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gravatar for Benjamin Dubreuil
4.5 years ago by
Benjamin Dubreuil20 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","mm usculus_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]]
ADD COMMENTlink modified 4.5 years ago by Steffen Durinck530 • written 4.5 years ago by Benjamin Dubreuil20
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gravatar for Steffen Durinck
4.5 years ago by
Steffen Durinck530 wrote:
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_homolo g_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_homo log_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 > [[alternative HTML version deleted]]
ADD COMMENTlink written 4.5 years ago by Steffen Durinck530
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: 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","m musculus_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","mm usculus_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 [[alternative HTML version deleted]]
ADD REPLYlink written 4.5 years ago by Benjamin Dubreuil20
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]]
ADD REPLYlink written 4.5 years ago by Thomas Maurel700
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