Retrieves gene annotation information given a vector of identifiers

This function retrieves gene annotations from Ensembl given a vector of identifiers. Annotation includes chromosome name, band, start position, end position, gene description and gene symbol. A wide variety of identifiers is available in Ensembl, these can be found with the listFilters function.

Usage

getGene(id, type, mart)

Arguments

id

vector of gene identifiers one wants to annotate

type

type of identifier, possible values can be obtained by the listFilters function. Examples are entrezgene_id, hgnc_symbol (for hugo gene symbol), ensembl_gene_id, unigene, agilentprobe, affy_hg_u133_plus_2, refseq_dna, etc.

mart

object of class Mart, containing connections to the BioMart databases. You can create such an object using the function useMart().

Author

Steffen Durinck

Examples

if (FALSE) { # interactive()
mart <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl")

# example using affy id
g <- getGene(id = "1939_at", type = "affy_hg_u95av2", mart = mart)
show(g)

# example using Entrez Gene id
g <- getGene(id = "100", type = "entrezgene_id", mart = mart)
show(g)
}