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.

     _w_r_i_t_e._r_e_s_l_t_s 'signature(x = "pumaPCARes-class")': writes the
          principal components for each array to a file. It takes the
          same arguments as 'write.table'. The argument "file" does not
          need to set any extension. The file name and extension "csv"
          will be added automatically. The default file name is "tmp". 

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

     Richard D. Pearson

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

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

