getHomolog {biomaRt} | R Documentation |
This function retrieves homologs of genes from one species in another species
getHomolog(id, from.type, to.type, from.array, to.array, from.species, to.species, mart, output = "martTable")
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 |
Sean Davis, Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck
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) }