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 retrieves information from two linked BioMart
     datasets

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

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

_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, representing the primary dataset on
          which filters apply .You can create such an object using the
          function useMart and update the mart object by selecting a
          dataset using the function useDataset.

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.

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

     Steffen Durinck

_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)
     }

