mapIdentifiers-methods       package:GSEABase       R Documentation

_M_e_t_h_o_d_s _f_o_r _F_u_n_c_t_i_o_n _m_a_p_I_d_e_n_t_i_f_i_e_r_s _i_n _P_a_c_k_a_g_e _G_S_E_A_B_a_s_e

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

     These methods convert the genes identifiers of a gene set from one
     type to another, e.g., from 'EntrezIdentifier' to
     'AnnotationIdentifier'. Methods can be called directly by the
     user; 'geneIdType<-' provides similar functionality.
     'verbose=TRUE'  produces warning messages when maps between
     identifier types are not 1:1, or a map has to be constructed on
     the fly (this situation does not apply when using the DBI-based
     annotation packages).

_M_e_t_h_o_d_s:

     The following methods are defined on 'what="GeneSet"':


     _w_h_a_t = "_A_N_Y", _t_o = "_A_N_Y", _f_r_o_m = "_A_N_Y", _v_e_r_b_o_s_e=_F_A_L_S_E This method
          warns of attempts to map 'from' and 'to' the same type, or
          generates an error if no suitable 'mapIdentifiers' methods
          are available.

     _w_h_a_t = "_G_e_n_e_S_e_t", _t_o = "_G_e_n_e_I_d_e_n_t_i_f_i_e_r_T_y_p_e", _f_r_o_m = "_m_i_s_s_i_n_g", _v_e_r_b_o_s_e=_F_A_L_S_E 
          This method will re-dispatch to a method with signature
          'signature(what=what, to=to, from=geneIdType(what))', and is
          present so that a user can call 'mapIdentifiers' without
          providing an explicit 'from' argument.

     _w_h_a_t = "_G_e_n_e_S_e_t", _t_o = "_G_e_n_e_I_d_e_n_t_i_f_i_e_r_T_y_p_e", _f_r_o_m = "_N_u_l_l_I_d_e_n_t_i_f_i_e_r", _v_e_r_b_o_s_e=_F_A_L_S_E 
          This maps a gene set from gene identifiers represented by the
          'NullIdentifier' type (i.e., no type associated with the
          genes) to gene identifiers represent by any class derived
          from 'GeneIdentifierType'.

     _w_h_a_t = "_G_e_n_e_S_e_t", _t_o = "_N_u_l_l_I_d_e_n_t_i_f_i_e_r", _f_r_o_m = "_G_e_n_e_I_d_e_n_t_i_f_i_e_r_T_y_p_e", _v_e_r_b_o_s_e=_F_A_L_S_E 
          This maps a gene set from gene identifiers represented by any
          'GeneIdentifierType' type to one represented by the
          'NullIdentifier' (i.e., no type associated with the genes).

     _w_h_a_t = "_G_e_n_e_S_e_t", _t_o = "_G_e_n_e_I_d_e_n_t_i_f_i_e_r_T_y_p_e", _f_r_o_m = "_e_n_v_i_r_o_n_m_e_n_t", _v_e_r_b_o_s_e=_F_A_L_S_E 
          Maps identifiers found in 'what' to the type described by
          'to', using the map (key-value pairs) found in 'from'.

     _w_h_a_t = "_G_e_n_e_S_e_t", _t_o = "_G_e_n_e_I_d_e_n_t_i_f_i_e_r_T_y_p_e", _f_r_o_m = "_A_n_n_D_b_B_i_m_a_p", _v_e_r_b_o_s_e=_F_A_L_S_E 
          Maps identifiers found in 'what' to the type described by
          'to', using the map (key-value pairs) found in 'from'.

     The following methods are defined for 'what=GeneColorSet'. These
     methods map gene- and phenotype color appropriately, and fail if
     coloring of gene identifiers involved in several-to-1 mappings
     conflict.

     _w_h_a_t = "_G_e_n_e_C_o_l_o_r_S_e_t", _t_o = "_G_e_n_e_I_d_e_n_t_i_f_i_e_r_T_y_p_e", _f_r_o_m = "_m_i_s_s_i_n_g", _v_e_r_b_o_s_e=_F_A_L_S_E 
          This method will re-dispatch to a method with signature
          'signature(what=what, to=to, from=geneIdType(what))', and is
          present so that a user can call 'mapIdentifiers' without
          providing an explicit 'from' argument.

     _w_h_a_t = "_G_e_n_e_C_o_l_o_r_S_e_t", _t_o = "_G_e_n_e_I_d_e_n_t_i_f_i_e_r_T_y_p_e", _f_r_o_m = "_N_u_l_l_I_d_e_n_t_i_f_i_e_r", _v_e_r_b_o_s_e=_F_A_L_S_E 
          This maps a gene set from gene identifiers represented by the
          'NullIdentifier' type (i.e., no type associated with the
          genes) to gene identifiers represent by any class derived
          from 'GeneIdentifierType'.

     _w_h_a_t = "_G_e_n_e_C_o_l_o_r_S_e_t", _t_o = "_N_u_l_l_I_d_e_n_t_i_f_i_e_r", _f_r_o_m = "_G_e_n_e_I_d_e_n_t_i_f_i_e_r_T_y_p_e", _v_e_r_b_o_s_e=_F_A_L_S_E 
          This maps a gene set from gene identifiers represented by any
          'GeneIdentifierType' type to one represented by the
          'NullIdentifier' (i.e., no type associated with the genes).

     _w_h_a_t = "_G_e_n_e_C_o_l_o_r_S_e_t", _t_o = "_G_e_n_e_I_d_e_n_t_i_f_i_e_r_T_y_p_e", _f_r_o_m = "_e_n_v_i_r_o_n_m_e_n_t", _v_e_r_b_o_s_e=_F_A_L_S_E 
          This method is not implemented, and exists to stop incorrect
          application of the 'GeneSet' method.

     _w_h_a_t = "_G_e_n_e_C_o_l_o_r_S_e_t", _t_o = "_G_e_n_e_I_d_e_n_t_i_f_i_e_r_T_y_p_e", _f_r_o_m = "_A_n_n_D_b_B_i_m_a_p", _v_e_r_b_o_s_e=_F_A_L_S_E 
          This method is not implemented, and exists to stop incorrect
          application of the 'GeneSet' method.

     A method exists for 'what="GeneSetCollection"':

     _w_h_a_t = "_G_e_n_e_S_e_t_C_o_l_l_e_c_t_i_o_n", _t_o = "_G_e_n_e_I_d_e_n_t_i_f_i_e_r_T_y_p_e", _f_r_o_m = "_m_i_s_s_i_n_g", _v_e_r_b_o_s_e = _F_A_L_S_E 
          Map each gene set in 'what' to gene identifier type 'to',
          using methods described above.

