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, gapAllowed = 500, alteredLow = 0.03, alteredHigh =
     0.97, spanLimit = 2e+07, recurrence = 75, thresholdType = c("quantile",
     "value")) 

_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'

gapAllowed: 'gapAllowed' is an integer specifying low threshold of base
          pair number to separate two adjacent segments, belower which
          the two segments will be joined as an altered span

alteredLow: 'alteredLow' is a positive number between 0 and 1
          specifying the lower reshold percential value. Only segments
          with values falling below this threshold are considered as
          altered span

alteredHigh: 'alteredHigh' is a positive number between 0 and 1
          specifying the upper reshold percential value. Only segments
          with values falling over this threshold are considered as
          altered span

recurrence: 'recurrence' is an integer between 1 and 100 that specifies
          the rate of occurrence for a gain or loss that are observed
          across sample. Only gains/losses with ocurrence rate grater
          than the threshold values are declared as MCRs

spanLimit: 

thresholdType: 'thresholdType' is a character string that can be either
          "quantile" or "value" indicating wether 'alteredLow' or
          'alteredHigh' is quantial or actual value

_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, gapAllowed = 500, alteredLow = 0.20,
                        alteredHigh = 0.80, recurrence = 50)

