getHomolog {biomaRt}R Documentation

Get homologs

Description

This function retrieves homologs of genes from one species in another species

Usage

getHomolog(id, from.type, to.type, from.array, to.array, from.mart, to.mart)

Arguments

id gene identifier
from.type type of identifier, value should be either entrezgene, embl or refseq
to.type type of identifier, value should be either entrezgene, embl or refseq
from.array Affy array from which the input identifiers come. Note if this has a value then you don't have to specify from.type and from.species.
to.array Affy array to which you want to map. Note if this has a value then you don't have to specify to.type and to.species.
from.mart Mart object using dataset from species of which the query id is from.
to.mart Mart object using dataset from species you want to find the homologs off.

Author(s)

Sean Davis, Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck

Examples

if(interactive()){
from.mart <- useMart("ensembl","hsapiens_gene_ensembl")
to.mart <- useMart("ensembl","mmusculus_gene_ensembl")

#HUGO to Entrez Gene

homolog = getHomolog(id = 1:20, from.mart = from.mart, to.mart = to.mart, from.type = 'entrezgene', to.type = 'refseq')
show(homolog)

#ensembl to ensembl

homolog = getHomolog( id = "ENSG00000072778", from.mart = from.mart, from.type = "ensembl", to.type="ensembl",to.mart=to.mart)
show(homolog)

#Affy to Affy

homolog = getHomolog( id = "1939_at", to.array = "affy_mouse430_2", from.array = "affy_hg_u95av2", from.mart = from.mart, to.mart=to.mart )
show(homolog)

#Ensembl to Affy

homolog = getHomolog( id = "ENSG00000072778", to.array = "affy_mouse430_2", from.type = "ensembl", from.mart = from.mart, to.mart = to.mart )
show(homolog)

}

[Package biomaRt version 1.8.2 Index]