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.mart, to.mart)
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. |
Sean Davis, Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck
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) }