runDNAcopy              package:snapCGH              R Documentation

_R_e_s_u_l_t_s _o_f _s_e_g_m_e_n_t_i_n_g _a_n _M_A_L_i_s_t _d_a_t_a _o_b_j_e_c_t _u_s_i_n_g _t_h_e _D_N_A_c_o_p_y _l_i_b_r_a_r_y

_D_e_s_c_r_i_p_t_i_o_n:

     The results of segmenting data from copy number array experiments
     from programs such as circular binary segmentation (CBS).  This
     function requires the library 'DNAcopy' to be loaded.

_U_s_a_g_e:

     runDNAcopy(input, smooth.region=2, outlier.SD.scale = 4, smooth.SD.scale = 2, trim=0.025, alpha = 0.01, p.method = c("hybrid", 
         "perm"), kmax = 25, nmin = 200, window.size = NULL, overlap = 0.25, undo.splits = c("none", "prune", "sdundo"), 
         undo.prune = 0.05, undo.SD = 3)

_A_r_g_u_m_e_n_t_s:

   input: An object of class 'MAList' or 'SegList'

smooth.region: number of points to consider on the left and the right
          of a point to detect it as an outlier.

outlier.SD.scale: the number of SDs away from the nearest point in the
          smoothing region to call a point an outlier.

smooth.SD.scale: the number of SDs from the median in the smoothing
          region where a smoothed point is positioned.

    trim: proportion of data to be trimmed for variance calculation for
          smoothing outliers and undoing splits based on SD.

   alpha: significance levels for the test to accept change-points.

p.method: method used for p-value computation.  For the "perm" method
          the p-value is based on full permutation.  For the "hybrid"
          method the maximum over the entire region is split into
          maximum of max over small segments and max over the rest. 
          Approximation is used for the larger segment max. Default is
          hybrid.

    kmax: the maximum width of smaller segment for permutation in the
          hybrid method.

    nmin: the minimum length of data for which the approximation of
          maximum statistic is used under the hybrid method.

window.size: size of window used to speed up computations when segment
          size is too large.  Default is NULL (whole segment used). If
          p.method is hybrid then this is set to NULL.

 overlap: proportion of data that overlap for adjacent windows.

undo.splits: A character string specifying how change-points are to be
          undone, if at all.  Default is "none".  Other choices are
          "prune", which uses a sum of squares criterion, and "sdundo",
          which  undoes splits that are not at least this many SDs
          apart.

undo.prune: the proportional increase in sum of squares allowed when
          eliminating splits if undo.splits="prune".

 undo.SD: the number of SDs between means to keep a split if
          undo.splits="sdundo".

_V_a_l_u_e:

     The function returns an object of class 'SegList'

_A_u_t_h_o_r(_s):

     Mike Smith, based upon DNAcopy help files written by E. S.
     Venkatraman and Adam Olshen

_S_e_e _A_l_s_o:

     'segment' 'MAList' 'runHomHMM' 'runGLAD' 'SegList'

