getFeature {biomaRt} | R Documentation |
This function function retrieves identifiers representing a certain gene given a gene symbol, chromosomal positions or GO identifier
getFeature( symbol, OMIMID, GOID, chromosome, start, end, type, mart)
symbol |
gene symbol |
OMIMID |
OMIM identifier |
GOID |
GO identifier |
chromosome |
chromosome, can be used without start and end positions |
start |
start on chromosome |
end |
end on chromosome |
type |
type of identifier that needs to be retrieved, possible values can be obtained by the listFilters function. Examples are entrezgene, hgnc_symbol (for hugo gene symbol), ensembl_gene_id, unigene, agilentprobe, refseq_dna, affy_hg_u133_plus_2, etc. |
mart |
object of class Mart, containing connections to the BioMart databases. You can creat such an object using the function martConnect. |
Steffen Durinck
if(interactive()){ mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") #example using affy id from Ensembl feat = getFeature( symbol = "TP53",type = "affy_hg_u95av2", mart = mart) show(feat) }