useMart               package:biomaRt               R Documentation

_C_o_n_n_e_c_t_s _t_o _t_h_e _s_e_l_e_c_t_e_d _B_i_o_M_a_r_t _d_a_t_a_b_a_s_e _a_n_d _d_a_t_a_s_e_t

_D_e_s_c_r_i_p_t_i_o_n:

     A first step in using the biomaRt package is to select a BioMart
     database and dataset to use.  The useMart function enables one to
     connect to a specified BioMart database and dataset within this
     database.  To know which BioMart databases are available see the
     listMarts function.  To know which datasets are available within a
     BioMart database, first select the BioMart database using useMart
     and then use the listDatasets function on the selected BioMart,
     see listDatasets function.

_U_s_a_g_e:

     useMart(biomart, dataset, host, user, password, port, local = FALSE, mysql=FALSE, archive=FALSE)

_A_r_g_u_m_e_n_t_s:

 biomart: BioMart database name you want to connect to. Possible
          database names can be retrieved with the functio listMarts

 dataset: Dataset you want to use.  To see the different datasets
          available within a biomaRt you can e.g. do:  mart =
          useMart('ensembl'), followed by listDatasets(mart).

   mysql: Boolean to specify if you want to access BioMart database via
          MySQL or via it's webservice of HTTP.  Default is using the
          webservice.

    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

    port: port to use in MySQL connection

   local: boolean to specify if you want to use a locally installed
          BioMart or a mirror BioMart database

 archive: Boolean to indicate if you want to access archived versions
          od BioMart databases.  This currently only works with
          mysql=TRUE and the ensembl BioMart database

_A_u_t_h_o_r(_s):

     Steffen Durinck,<URL: http://www.stat.berkeley.edu/~steffen>

_E_x_a_m_p_l_e_s:

     if(interactive()){

     mart = useMart("ensembl")
     mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

     }

