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 is the main biomaRt query function.  Given a set of
     filters and corresponding values, it retrieves the user specified
     attributes from the BioMart database one is connected to

_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, uniqueRows = TRUE)

_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 (one or more) 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. vector of affy IDs.  If multiple
          filters are specified then the argument should be a list of
          vectors of which the position of each vector corresponds to
          the position of the filters in the filters argument.

    mart: object of class Mart, created with the useMart function.

    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.

uniqueRows: If the result of a query contains multiple identical rows,
          setting this argument to TRUE (default) will result in
          deleting the duplicated rows in the query result at the
          server side.

_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")
     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)

     }

