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))]]

