hbTests-methods           package:GGtools           R Documentation

_h_a_p_l_o_t_y_p_e-_b_l_o_c_k _b_a_s_e_d _t_e_s_t_s _f_o_r _s_t_r_u_c_t_u_r_e_d _e_x_p_r_e_s_s_i_o_n _v_a_r_i_a_t_i_o_n

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

     haplotype-block based tests for structured expression variation

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



     _f_m_l_a = "_g_e_n_e_s_y_m", _s_m_s = "_s_m_l_S_e_t", _c_n_u_m = "_c_h_r_n_u_m", _r_s_i_d = "_n_u_m_e_r_i_c", _r_a_d = "_n_u_m_e_r_i_c" 
          expression data for gene identified by 'genesym' is extracted
          from 'sms', and genotype data within 'rad' base pairs of
          'rsid' are obtained and processed by 'mapLD' to define
          haplotype blocks and the SNP tagging these blocks.  Score
          tests are then computed for the association of expression of
          the gene identified by 'genesym' with haplotype copy number
          (additive model by default, but options captured by ... are
          passed to 'haplo.score'.)


_E_x_a_m_p_l_e_s:

     library(GGtools)
     data(hmceuB36.2021)
     hmFou = hmceuB36.2021[, hmceuB36.2021$isFounder==TRUE]
     hh = hbTests(genesym("CPNE1"), hmFou, chrnum(20), 33600000, 2e4 )
     hh
     pvals(hh)
     plot(locs(hh), -log10(pvals(hh)))
     hscores(hh)[[which.min(pvals(hh))]]

