classificationModelSignalTrans package:gene2pathway R Documentation

_H_i_e_r_a_r_c_h_i_c_a_l _C_l_a_s_s_i_f_i_c_a_t_i_o_n _M_o_d_e_l _f_o_r _S_i_g_n_a_l_i_n_g _T_r_a_n_s_d_u_c_t_i_o_n _P_a_t_h_w_a_y_s _a_n_d _P_a_t_h_w_a_y _C_o_m_p_o_n_e_n_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     This file contains the hierarchical classification model to
     predict KEGG signaling pathways and pathway components for genes.
     The model contains only pathway components, to which a specified
     minimum number of genes could be mapped in the training phase (see
     'retrain.signaltrans'). Important: There exists one separate model
     file for each organism.

_F_o_r_m_a_t:

     List of class "model", where each model has the following entries:

     _W learned decision hyperplane normal vector

     _C dictionary of label vectors, which can be predicted individually
          or which can be used to predict combinations of them

     _d_e_t_e_c_t_o_r_s SVM models trained to separate one specific pathway
          branch from the rest of the hierarchy

     _u_s_e_d__d_o_m_a_i_n_s InterPro domains used by the classifier to separate
          the specific branch from the rest of the hierarchy

     _a_l_l_d_o_m_a_i_n_s all InterPro domains used to build feature vectors

     _a_l_l_p_a_t_h_w_a_y_s hierarchy branches, which can be predicted

     _t_r_e_e_s_i_z_e_s" relative size of hierarchy below the corresponding
          branch

     _k_e_g_g__h_i_e_r_a_r_c_h_y a nested list with information (parent branches,
          pathway names, pathway IDs, hierarchy level) on all higher
          hierarchy branches for each pathway

     _e_l_e_m_I_D_s a list of KEGG element IDs mapping to each pathway
          component - may be used to highlight pathway components with
          'color.pathway.by.elements'.

_A_u_t_h_o_r(_s):

     Holger Froehlich

_S_e_e _A_l_s_o:

     'classificationModel'

