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.

     Other functions which operate on 'SegList' objects include:
     'plotSegmentationStates'

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

     Mike Smith

