DNAcopy-internal           package:DNAcopy           R Documentation

_I_n_t_e_r_n_a_l _D_N_A_c_o_p_y _f_u_n_c_t_i_o_n_s

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

     Internal functions of package DNAcopy.

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

     changepoints(genomdat, data.type = "logratio", alpha = 0.01, nperm
                      = 10000, window.size = NULL, overlap = 0.25, trim =
                      0.025, smooth.outliers = TRUE, smooth.region = 2,
                      outlier.SD = 4, smooth.SD = 2, smooth.output = FALSE,
                      undo.splits = "none", undo.prune = 0.05, undo.SD = 3,
                      verbose = TRUE)
     changepoints.prune(genomdat, lseg, change.cutoff=0.05)
     changepoints.sdundo(genomdat, lseg, change.SD=3, trim=0.025)
     smooth.data(genomdat, smooth.region = 2, outlier.SD = 4,
                      smooth.SD = 2, trim = 0.025)
     trimmed.variance(genomdat, trim=0.025)
     inflfact(trim)

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

     These are not to be called directly by the user

