qb.BayesFactor            package:qtlbim            R Documentation

_B_a_y_e_s_i_a_n _m_o_d_e_l _s_e_l_e_c_t_i_o_n _v_i_a _B_a_y_e_s _f_a_c_t_o_r_s.

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

     Model-averaged posteriors and Bayes factors computed for number
     and pattern of QTL, chromosomes and pairs of chromosomes showing
     epistasis.

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

     qb.BayesFactor(qbObject, items = c("nqtl","pattern","chrom","pairs"),
       cutoff.pattern = 0.2, cutoff.pairs = 1, nmax = 15)
     ## S3 method for class 'qb.BayesFactor':
     plot(x, ...)
     ## S3 method for class 'qb.BayesFactor':
     summary(object, sort = TRUE, digits = 3, ...)
     ## S3 method for class 'qb.BayesFactor':
     print(x, ...)

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

qbObject: An object of class 'qb'.

  object: Object of class 'qb.BayesFactor'.

       x: Object of class 'qb.BayesFactor'.

   items: Items to include in model selection assessment.

cutoff.pattern: Percent cutoff for pattern inclusion in model
          selection.

cutoff.pairs: Percent cutoff for epistatic pair inclusion in model
          selection.

    nmax: Maximum number of model terms included per item (for 'items'
          "pattern" and "pairs" only).

    sort: Sort by Bayes factor if 'TRUE'.

  digits: Number of significant digits for summary.

     ...: Additional arguments passed to generic plot, summary or
          print.

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

     'qb.BayesFactor' creates model selection results for selected
     items. These are based on marginal posteriors and priors, averaged
     over all other model parameters. The posterior may be influenced
     by prior, while Bayes factors are empirically less sensitive for
     QTL model selection.  The Bayes factors are computed relative to
     the smallest term for each item, using the ratios of
     'posterior/prior'. Any pair of model terms can be compared as the
     ratio of their Bayes factors. The 'items' evaluated are:

_n_q_t_l Number of QTLs.

_p_a_t_t_e_r_n Pattern of QTL across chromosomes. Identifiers are
     comma-separated chromosome numbers, with asterisk 'n*' for
     multiple QTL per chromosome.

_c_h_r_o_m Chromosome.

_p_a_i_r_s Epistatic pairs of chromosomes.

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

     List with 'items', each containing: 

posterior: Posterior frequency of MCMC samples.

   prior: Prior frequency.

      bf: Rank-ordered Bayes factors relative to smallest value.

    bfse: Approximate standard error for bf computed using binomial
          variance of MCMC samples.

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

     Brian S. Yandell, yandell@stat.wisc.edu

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.qtlbim.org>

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

     'plot.qb', 'qb.mcmc'

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

     temp <- qb.BayesFactor(qbExample)
     summary(temp)
     plot(temp)

