martConnect {biomaRt} | R Documentation |
This function connects to available BioMarts
martConnect(biomarts = "ensembl", host, user, password, mart, local = FALSE)
biomarts |
vector with BioMart database names you want to connect to. Use one or a vector of the following BioMart database names: ensembl (default, for gene information, GO and OMIM annotation),sequence (for sequence retrieval), snp (for SNP retrieval), uniprot (for protein related data), vega (for VEGA gene annotation) |
host |
If you want to use a local host or a miror database, use vector of hosts. For connecting to public BioMarts this parameter is not required |
user |
username, use vector of usernames for non public or miror BioMarts |
password |
password, use vector of passwords for non-public or miror BioMarts |
mart |
Mart object, use if you want to add a connection to a BioMart to an existing Mart object |
local |
boolean to specify if you want to use a locally installed BioMart or a mirror BioMart database |
Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck
if(interactive()){ mart <- martConnect(biomarts = c("ensembl","sequence")) martDisconnect(mart = mart) }