findAmplif.func             package:aCGH             R Documentation

_F_u_n_c_t_i_o_n _t_o _d_e_t_e_r_m_i_n_e _h_i_g_h _l_e_v_e_l _a_m_p_l_i_f_i_c_a_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function identifies high level amplifications by considering
     the height, the width of an amplicon relative to the urrounding
     clones. Only narrow peaks much higher than its neigbors are
     considered as high level amplifications.

_U_s_a_g_e:

     findAmplif.func(absValSingle = 1, absValRegion = 1.5, diffVal1 = 1,
     diffVal2 = 0.5, maxSize = 10000, translen.matr = res3$translen.matrix,
     trans.matr = res3$trans.matr, aber = res2$aber, outliers = res1$outlier,
     pred = res1$pred.out, pred.obs = res1$pred.obs.out, statesres =
     states.bic)

_A_r_g_u_m_e_n_t_s:

absValSingle: A clone is declared to be an amplification if it is a
          focal aberration or an outlier and its value exceeds
          absValSingle

absValRegion: A clone is an amplification if if a clone belong to a
          region with width less than maxSize and  observed value for a
          clones is greater than absValRegion

diffVal1: Clone is an amplification if it is an aberration and greater
          by diffVal1 than max of the two surrounding stretches

diffVal2: Clone is an amplification if it is an outlier, its observed
          values is greater by diffVal2 than max of the two surrounding
          stretches

 maxSize: The clones  may not be declared as amplifications if they
          belong to the states with spanning more than maxSize

translen.matr: State length matrix. The output of the 'findTrans.func'

trans.matr: Transition matrix. The output of the 'findTrans.func'

    aber: Aberration matrix. The output of the 'findAber.func'

outliers: Outliers matrix. The output of the 'findOutliers.func'

    pred: Predicted values matrix. The output of the
          'findOutliers.func'

pred.obs: Predicted values matrix with observed values assigned to the
          outliers. The output of the 'findOutliers.func'

statesres: The states output of the 'hmm.run.func'

_D_e_t_a_i_l_s:

     Note that all the distances are in Megabases and all the heights
     are on log2ratio scale.

_V_a_l_u_e:

amplif.matrix: Binary matrix with a row for each clone and column for
          each sample. "1" indicates amplification

     ...

_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'

