cghMCR-class             package:cghMCR             R Documentation

_C_l_a_s_s "_c_g_h_M_C_R" _i_s _a _S_4 _c_l_a_s_s _f_o_r _t_h_e _i_d_e_n_t_i_f_i_c_a_t_i_o_n _o_f _m_i_n_i_m_u_m
_c_o_m_m_o_n _r_e_g_i_o_n_s _o_f _g_a_i_n_s _o_r _l_o_s_s_e_s _a_c_r_o_s_s _s_a_m_p_l_e_s

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

     Objects of this class provides the functionalities to detecting
     chromosome regions that show gains or losses across differnet
     samples

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("cghMCR", ...)'.
     A constructor 'cghMCR' may be used to instantiate object of this
     class

_S_l_o_t_s:


     '_D_N_A_S_e_g': Object of class '"data.frame"' containing segmentation
          data derived from segmentation analysis using segment or
          'getSegments'

     '_g_a_p_A_l_l_o_w_e_d': Object of class '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 

     '_a_l_t_e_r_e_d_L_o_w': Object of class '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 

     '_a_l_t_e_r_e_d_H_i_g_h': Object of class '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 

     '_r_e_c_u_r_r_e_n_c_e': Object of class '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 or losses
          with ocurrence rate grater than the threshold values are
          declared as MCRs

     '_s_p_a_n_L_i_m_i_t': Object of class 'spanLimit' is an integer that
          defines the leangh of altered spans that can be considered as
          locus. It is not of any use at this time

_M_e_t_h_o_d_s:


     _M_C_R 'signature(object = "cghMCR")': identifies minimum common
          regions of gains/losses across samples

_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

_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)

