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.species, to.species, mart, output = "martTable")

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.species species of which the id is from. Accepted values for species can be retrieved with the function getSpecies()
to.species species in which you want to find the homologs. Accepted values for species can be retrieved with the function getSpecies()
mart object of class Mart, containing connections to the BioMart databases. You can creat such an object using the function martConnect.
output desired output type, object of class martTable

Author(s)

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

See Also

Examples

if(interactive()){
mart <- martConnect()

#HUGO to Entrez Gene

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

#ensembl to ensembl

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

#Affy to Affy

homolog = getHomolog( id = "1424184_at", to.array = "hg_u95av2", from.array = "mouse430a_2", mart = mart )
show(homolog)

#Affy to ensembl

homolog = getHomolog( id = "1424184_at", to.species = "hsapiens", to.type = "ensembl", from.array = "mouse430a_2", mart = mart )
show(homolog)

martDisconnect(mart = mart)
}

[Package biomaRt version 1.4.0 Index]