getLDS                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_w_o _l_i_n_k_e_d _d_a_t_a_s_e_t_s

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

     This function is the main biomaRt query function that links 2
     datasets and retrieves information from these linked BioMart
     datasets.  In Ensembl this translates to homology mapping.

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

     getLDS(attributes, filters = "", values = "", mart, attributesL, filtersL = "", valuesL = "", martL, verbose = FALSE, uniqueRows = TRUE)

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

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

 filters: Filters that should be used in the query. These filters will
          be applied to primary dataset.  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 created with the useMart function.

attributesL: Attributes of linked dataset that needs to be retrieved

filtersL: Filters to be applied to the linked dataset

 valuesL: Values for the linked dataset filters

   martL: Mart object representing linked dataset

 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: Logical to indicate if the BioMart web service should
          return unique rows only or not.  Has the value of either TRUE
          or FALSE

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

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

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

     if(interactive()){
     human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
     mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl") 
     getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), filters = "hgnc_symbol", values = "TP53", mart = human, attributesL = c("chromosome_name","start_position"), martL = mouse)
     }

