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="www.biomart.org", path="/biomart/martservice", port=80, archive=FALSE, local = FALSE, mysql = FALSE, user, password)

_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).

    host: Host to connect to if different then www.biomart.org

    path: Path that should be pasted after to host to get access to the
          web service URL

    port: port to connect to, will be pasted between host and path

 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

   local: MySQL access to Ensembl is no longer supported.  biomaRt  in
          web service mode supports all BioMart queries.  Local BioMart
          databases can be accessed by specifying the local host which
          runs the local BioMart web service.

   mysql: MySQL access to Ensembl is no longer supported.  biomaRt  in
          web service mode supports all BioMart queries.  Local BioMart
          databases can be accessed by specifying the local host which
          runs the local BioMart web service.

    user: MySQL access to Ensembl is no longer supported.  biomaRt  in
          web service mode supports all BioMart queries.  Local BioMart
          databases can be accessed by specifying the local host which
          runs the local BioMart web service.

password: MySQL access to Ensembl is no longer supported.  biomaRt  in
          web service mode supports all BioMart queries.  Local BioMart
          databases can be accessed by specifying the local host which
          runs the local BioMart web service.

_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")
     }

