gwSnpScreen-methods         package:GGtools         R Documentation

_g_e_n_o_m_e-_w_i_d_e _t_e_s_t _f_o_r _a_s_s_o_c_i_a_t_i_o_n _b_e_t_w_e_e_n _S_N_P _a_n_d _p_h_e_n_o_t_y_p_e

_D_e_s_c_r_i_p_t_i_o_n:

     genome-wide test for association between SNP and phenotype

_M_e_t_h_o_d_s:


     _s_y_m = "_g_e_n_e_s_y_m", _s_m_s = "_s_m_l_S_e_t", _c_n_u_m="_c_n_u_m_O_r_M_i_s_s_i_n_g" 'sym' is an
          instance of 'genesym' class (typically just a wrapped
          character string giving a SYMBOL value for the expression
          annotation package in use, or a GeneSet instance, see below);
          'sms' is an integrative instance of 'smlSet' containing
          snp.matrix genotype data in a list and coordinated expression
          data. Restriction of analysis to specific chromosomes can be
          accomplished by passing an instance of 'chrnum' as the third
          argument.

          The 'gwSnpScreen' computes the snp.rhs.tests from snpMatrix
          for all snp against the specified expression phenotype.

          If 'sym' is an instance of the GSEABase GeneSet class, a list
          of gwSnpScreenResults is packaged in a multiGwSnpScreenResult
          instance.

_E_x_a_m_p_l_e_s:

     data(hmceuB36.2021)
     objects("package:GGBase")
     g1 = gwSnpScreen( genesym("CPNE1"), hmceuB36.2021, chrnum(20) )
     g1
     plot(g1)

