cghMCR                package:cghMCR                R Documentation

_T_h_e _c_o_n_s_t_r_u_c_t_o_r _f_o_r _t_h_e _c_g_h_M_C_R _c_l_a_s_s

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

     Instantiates a cghMCR object using the parameters passed.

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

     cghMCR(segments, margin = 0, gain.threshold = 0.5, loss.threshold = -0.5)

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

segments: 'segments' is a data frame extracted from the "output"
          element of the object returned by segment of the package
          DNAcopy or 'getSegments'

  margin: 'margin' is a integer specifying how far apart two adjacent
          segments are allowed to be considered to be the same locus 

gain.threshold: 'gain.threshold' is a positive integer specifying the
          reshold log2 ratio when a segment of chromosome can be
          considered to be a gain

loss.threshold: 'loss.threshold' is a negative integer specifying the
          reshold log2 ratio when a segment of chromosome can be
          considered to be a loss

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

     The function is just a constructor of the 'cghMCR' class for the
     instantiation of a cghMCR object

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

     An object of the cghMCR class

_N_o_t_e:

     The function is a contribution of The Center for Applied Cancer
     Science of Dana-Farber Cancer Institute

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

     Jianhua Zhang

_R_e_f_e_r_e_n_c_e_s:

     References on S4 class

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

     'cghMCR'

_E_x_a_m_p_l_e_s:

       require("cghMCR")
       data("sampleData")
       segments <- getSegments(sampleData)
       cghmcr <- cghMCR(segments, margin = 0, gain.threshold = 0.8,
                      loss.threshold = -0.8)

