bayesint                 package:qtl                 R Documentation

_B_a_y_e_s_i_a_n _c_r_e_d_i_b_l_e _i_n_t_e_r_v_a_l

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

     Calculate an approximate Bayesian credible interval for a
     particular chromosome, using output from 'scanone'.

_U_s_a_g_e:

     bayesint(results, chr, qtl.index, prob=0.95, lodcolumn=1, expandtomarkers=FALSE)

_A_r_g_u_m_e_n_t_s:

 results: Output from 'scanone', or a qtl object as output from
          'refineqtl'.

     chr: A chromosome ID (if input 'results' are from 'scanone'.

qtl.index: Numeric index for a QTL (if input 'results' are from
          'refineqtl'.

    prob: Probability coverage of the interval.

lodcolumn: An integer indicating which of the LOD score columns should
          be considered (if input 'results' are from 'scanone').

expandtomarkers: If TRUE, the interval is expanded to the nearest
          flanking markers.

_D_e_t_a_i_l_s:

     We take 10^LOD, rescale it to have area 1, and then calculate the
     connected interval with density above some threshold and having
     coverage matching the target probability.

_V_a_l_u_e:

     An object of class 'scanone' indicating the estimated QTL position
     and the approximate endpoints for the Bayesian credible interval.

_A_u_t_h_o_r(_s):

     Karl W Broman, kbroman@biostat.wisc.edu

_S_e_e _A_l_s_o:

     'scanone', 'lodint'

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

     data(hyper)

     hyper <- calc.genoprob(hyper, step=0.5)
     out <- scanone(hyper, method="hk")
     bayesint(out, chr=1)
     bayesint(out, chr=4)
     bayesint(out, chr=4, prob=0.99)
     bayesint(out, chr=4, expandtomarkers=TRUE)

