pumaPCARes-class            package:puma            R Documentation

_C_l_a_s_s _p_u_m_a_P_C_A_R_e_s

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

     This is a class representation for storing the outputs of the
     pumaPCA function. Objects of this class should usually only be
     created through the 'pumaPCA' function.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("pumaPCARes",
     ...)'.

_S_l_o_t_s:

     '_m_o_d_e_l': Object of class "pumaPCAModel" representing the model
          parameters

     '_e_x_p_e_c_t_a_t_i_o_n_s': Object of class "pumaPCAExpectations" representing
          the model expectations

     '_v_a_r_Y': Object of class "matrix" representing the variance in the
          expression levels

     '_Y': Object of class "matrix" representing the expression levels

     '_p_h_e_n_o_D_a_t_a': Object of class "AnnotatedDataFrame" representing the
          phenotype information

     '_t_i_m_e_T_o_C_o_m_p_u_t_e': Object of class "numeric" representing the time
          it took 'pumaPCA' to run

     '_n_u_m_b_e_r_O_f_I_t_e_r_a_t_i_o_n_s': Object of class "numeric" representing the
          number of iterations it took 'pumaPCA' to converge

     '_l_i_k_e_l_i_h_o_o_d_H_i_s_t_o_r_y': Object of class "list" representing the
          history of likelihood values while 'pumaPCA' was running

     '_t_i_m_i_n_g_H_i_s_t_o_r_y': Object of class "list" representing the history
          of how long each iteration took while 'pumaPCA' was running

     '_m_o_d_e_l_H_i_s_t_o_r_y': Object of class "list" representing the history of
          how the model was changing while 'pumaPCA' was running

     '_e_x_i_t_R_e_a_s_o_n': Object of class "character" representing the reason
          'pumaPCA' halted. Can take the values "Update of Likelihood
          less than tolerance x", "Update of W less than tolerance x",
          "Iterations exceeded", "User interrupt", "unknown exit
          reason"

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

     _p_l_o_t 'signature(x="pumaPCARes-class")': plots two principal
          components on a scatter plot.

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

     Richard D. Pearson

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

     Related method 'pumaPCA' and related class 'pumaPCARes'.

