dataSource         package:domainsignatures         R Documentation

_C_o_n_t_r_u_c_t_o_r _f_o_r _a_n_n_o_t_a_t_i_o_n _o_b_j_e_c_t

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

     This function creates the necessary annotation object of class
     'ipDataSource' containing the pathway and InterPro ID mappings.

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

     dataSource(mapping, type = "generic")

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

 mapping: A named list providing a mapping between enterzgene
          identifiers and arbitrary groupings of genes or pathways.

    type: The type of pathway. A character skalar.

_D_e_t_a_i_l_s:

     For genes without pathway membership, 'NA' list items need to be
     included in 'mapping'. The names of the list comprise the gene
     universe to test against. The function will access the ensembl
     'biomaRt' database in order to retrieve the necessary InterPro
     domain information.

_V_a_l_u_e:

     Object of class 'ipDataSource'

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

     Florian Hahne

_S_e_e _A_l_s_o:

     'gseDomain', 'getKEGGdata'

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

     grouping <- list("653361"=c("pw1", "pw2"), "729230"="pw1",
                      "415117"="pw3") 
     dataSource(grouping)

