gwSnpScreenResult-class       package:GGtools       R Documentation

_C_l_a_s_s "_g_w_S_n_p_S_c_r_e_e_n_R_e_s_u_l_t" - _c_o_n_t_a_i_n_e_r_s _f_o_r
_g_e_n_o_m_e-_w_i_d_e _a_n_d _c_h_r_o_m_o_s_o_m_e-_w_i_d_e _s_n_p _s_c_r_e_e_n _s_t_a_t_i_s_t_i_c_s

_D_e_s_c_r_i_p_t_i_o_n:

     Class "gwSnpScreenResult" - containers for genome-wide and
     chromosome-wide snp screen statistics

_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("gwSnpScreenResult", ...)'. Mild extensions to 'list'.

_S_l_o_t_s:


     '._D_a_t_a': Object of class '"list"' list of data.frames or matrices
          of test results 

     '_g_e_n_e': Object of class '"character"' gene name 

     '_p_s_i_d': Object of class '"character"' probe identifier 

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"' - propagated from
          smlSet 

     '_s_n_p_L_o_c_E_x_t_R_e_f': Object of class '"character"', full pathname of
          external store for snp locations relevant to the smlSet
          instance from which gwSnpScreenResult was computed.

_E_x_t_e_n_d_s:

     Class '"list"', from data part. Class '"vector"', by class "list",
     distance 2. Class '"AssayData"', by class "list", distance 2.

_M_e_t_h_o_d_s:


     _p_l_o_t 'signature(x = "gwSnpScreenResult", y = "ANY")':  plots minus
          log p values of association tests along chromosomal
          coordinates

     _s_h_o_w 'signature(object = "gwSnpScreenResult")': brief report 

     [ 'signature(object = "gwSnpScreenResult")': restricts chromosomes
          represented 

_A_u_t_h_o_r(_s):

     VJ Carey <stvjc@channing.harvard.edu>

_E_x_a_m_p_l_e_s:

     showClass("gwSnpScreenResult")
     data(hmceuB36.2021)
     objects("package:GGBase")
     x = gwSnpScreen(genesym("CPNE1"), hmceuB36.2021, chrnum(20))
     x

