SegList-class            package:snapCGH            R Documentation

_S_e_g_m_e_n_t_a_t_i_o_n _S_t_a_t_e_s - _c_l_a_s_s

_D_e_s_c_r_i_p_t_i_o_n:

     A list based class for storing the results of a segmentation
     algorithm. They are generally created by running one of the
     following functions 'runHomHMM', 'runGLAD' or 'runDNAcopy' on an
     'MAList object'.

_S_l_o_t_s/_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     Objects should contain the following list components:

       'pred':         Predicted value of the state.
       'disp':         Dispersion.
       'obs':          Observed value.
       'state':        Numeric value.
       'nstates.hmm':  The number of states per chromosome.  Each row represents a chromosome and each column is an array.
       'genes':        data.frame that contains the chromosome and position on the chromosome for each clone.  Used for plotting functions.

     Optional:

       'rpred':  Smoothed value for the clone.
       'prob':   Probability of the clone being in the assigned state.

_M_e_t_h_o_d_s:

     'SegLists' can be subsetted and combined.  They also return
     dimensions so functions such as 'dim', 'nrow' and 'ncol' are also
     defined.  'SegList' inherits the 'show' method from the Limma
     class 'LargeDataObject'.  This means that the 'SegList' will print
     in a relatively compact way.

_A_u_t_h_o_r(_s):

     Mike Smith

