computeSD              package:snapCGH              R Documentation

_F_u_n_c_t_i_o_n _t_o _e_s_t_i_m_a_t_e _e_x_p_e_r_i_m_e_n_t_a_l _v_a_r_i_a_b_i_l_i_t_y _o_f _a _s_a_m_p_l_e

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

     This functions estimate experimental variability of a given
     sample. This value can be used to rank samples in terms of the
     quality as well as to derive thresholds for declaring gained and
     lost clones.

_U_s_a_g_e:

     computeSD(segList, maxmadUse = 0.2, maxmedUse = 0.2,
                    maxState = 3, maxStateChange = 10, minClone = 5,
                    maxChrom = 22)

_A_r_g_u_m_e_n_t_s:

 segList: Object of class 'SegList'. 

maxmadUse: Maximum median absolute deviation allowed to controbute to
          the overall variability calculation. 

maxmedUse: Maximum median value for a state allowed to contribute to
          the calculation. 

maxState: Maximum number of the states on a given chromosome for the
          states from that chromosome to be allowed to enter noise
          variability calculation. 

maxStateChange: Maximum number of changes from state to state on a
          given chromosome for that chromosome to enter  noise
          variability calculation. 

minClone: Minimum number of clones in a state for clones in that sate
          to enter variability calculation. 

maxChrom: Maxiumum chromosomal index (generally only autosomes are used
          for this calculation. 

_D_e_t_a_i_l_s:

     Median absolute deviation is estimated in all the states passing
     the criteria defined by the parameters of the function. Then
     median of all MADs on individual chromosomes as well as across all
     chromosomes is taken to estimate chromosomal  experimental
     variability and sample experimental variability.

_V_a_l_u_e:

madChrom: Returns a matrix containing estimated variability for each
          chromosome for each sample.

madGenome: Returns a vector with estimate of experimental varibility
          for each sample.

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

     Mike Smith

_R_e_f_e_r_e_n_c_e_s:

     Application of Hidden Markov Models to the analysis of the array
     CGH data, Fridlyand et.al., _JMVA_, 2004

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

     'SegList'

