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)

