getBM                package:biomaRt                R Documentation

_R_e_t_r_i_e_v_e_s _i_n_f_o_r_m_a_t_i_o_n _f_r_o_m _t_h_e _B_i_o_M_a_r_t _d_a_t_a_b_a_s_e

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

     This function retrieves information from the BioMart database

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

     getBM(attributes, filters = "", values = "", mart, curl = NULL, output = "data.frame", list.names = NULL, na.value = NA, checkFilters = TRUE, verbose = FALSE)

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

attributes: Attributes you want to retrieve.  A possible list of
          attributes can be retrieved using the function
          listAttributes.

 filters: Filters that should be used in the query.  A possible list of
          filters can be retrieved using the function listFilters.

  values: Values of the filter, e.g. list of affy IDs

    mart: object of class Mart, containing connections to the BioMart
          databases.  You can creat such an object using the function
          useMart and update the mart object by selecting a dataset
          using the function useDataset.

    curl: An optional 'CURLHandle' object, that can be used to speed up
          getBM when used in a loop.

  output: Determines the output of getBM which can be either a
          data.frame (default) or a list.

list.names: In case a list was selected as output the different
          elements in the list can be given user defined names with
          this argument

na.value: In case a list was selected as output, the value of na.value
          will used when missing elements are present in the output

checkFilters: Sometimes attributes where a value needs to be specified,
          for example upstream_flank with value 20 for obtaining
          upstream sequence flank regions of length 20bp, are treated
          as filters in BioMarts.  To enable such a query to work, one
          must specify the attribute as a filter and set checkFilters =
          FALSE for the query to work.

 verbose: When using biomaRt in webservice mode and setting verbose to
          TRUE, the XML query to the webservice will be printed. 
          Alternatively in MySQL mode the MySQL query will be printed.

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

     Steffen Durinck

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

     if(interactive()){
     mart <- useMart("ensembl")
     datasets <- listDatasets(mart)
     mart<-useDataset("hsapiens_gene_ensembl",mart)
     getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name","band"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_at"), mart=mart)

     }

