computeSD.func             package:aCGH             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.Samples(aCGH.obj, maxChrom = 22, maxmadUse = .3,
                       maxmedUse = .5, maxState = 3, maxStateChange = 100,
     minClone = 20)
     computeSD.func(statesres = states.bic, maxmadUse = 0.2, maxmedUse = 0.2,
                    maxState = 3, maxStateChange = 100, minClone = 20,
                    maxChrom = 22)

_A_r_g_u_m_e_n_t_s:

aCGH.obj: Object of class 'aCGH'. 

statesres: The states.hmm object, generally is the output of
          'mergeFunc'. 

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):

     Jane Fridlyand

_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:

     'aCGH'

