Retrieves gene annotation information given a vector of identifiers
This function retrieves gene annotations from Ensembl given a vector of identifiers. Annotation includes chromsome 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.
getGene( id, type, mart)
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. |
Steffen Durinck
if(interactive()){
mart = useMart("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)
}Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.