findAmplifications          package:snapCGH          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:

     findAmplifications(segList, 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)

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

 segList: An object of class 'SegList'

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
          'findTranslocations'

trans.matr: Transition matrix. The output of the 'findTranslocations'

    aber: Aberration matrix. The output of the 'findAberrations'

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

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

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

_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:

