removeBreakpoints            package:GLAD            R Documentation

_R_e_m_o_v_e _b_r_e_a_k_p_o_i_n_t_s

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

     This function optimizes the number of breakpoints.

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

     removeBreakpoints.profileChr(profileChr, lambda=10, type="tricubic", param=c(d=6), verbose=FALSE, ...)
     removeLevel.profileChr <- function(profileChr, lambda=10, ...)

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

profileChr: Object of class 'profileChr'.

  lambda: Penalty term (lambda') used during the  "Optimization of the
          number of breakpoints" step.

    type: Type of kernel used in the penalty term.

   param: Parameter for the kernel used in the penalty term.

 verbose: If 'TRUE' some information are printed

     ...: Argument to be passed to 'detectOutliers', typically 'alpha'.

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

     The function 'removeBreakpoints' uses the results of
     'chrBreakpoints' and optimizes the number of breakpoints
     previously detected: when a breakpoint is removed, then it is
     flagged out by -1 in the vector 'Breakpoints' of the data.frame
     attribute of the object of class 'profileChr'. 'removeBreakpoints'
     is used within the global function 'glad'.

_V_a_l_u_e:

     Data frame.

_A_u_t_h_o_r(_s):

     Philippe Hup, <URL: Philippe.Hupe@curie.fr>.

_S_e_e _A_l_s_o:

     'chrBreakpoints','glad', 'kernelpen'.

