qb.model               package:qtlbim               R Documentation

_S_e_t _u_p _i_n_t_e_r_a_c_t_i_n_g _Q_T_L _m_o_d_e_l _f_o_r _q_b._m_c_m_c

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

     This function sets up a genome-wide interacting QTL model by
     specifying global constraints on models and priors on unknowns.

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

     qb.model(cross, epistasis = TRUE, main.nqtl = 3,
       mean.nqtl = main.nqtl + 3, max.nqtl = NULL, interval = NULL,
       chr.nqtl = NULL,intcov = c(0), depen = FALSE,
       prop = c(0.5, 0.1, 0.05), ...)           
       

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

   cross: An object of class 'cross'. See 'read.cross' for details. 

epistasis: indicates if epistasis is included in the model: TRUE or
          FALSE

main.nqtl: prior expected number of main effect QTLs. 

mean.nqtl: prior expected number for all QTLs on all chromosomes
          including  QTLs with main effects, epistatic effects and
          gene-environment interactions.

max.nqtl: maximum number of QTLs allowed in the model. Default is
          l+3sqrt{l} where l is 'main.qtl' for non-epistatic model and
          'mean.qtl' for epistatic model. 

interval: minimum distance between any two flanking QTLs for all
          chromosomes. Default is the average distance between markers
          in each chromosome.

chr.nqtl: list of the maximum number of QTLs allowed to be detected  on
          each chromosome. Default is the length of the chromosome
          divided by 'interval'.

  intcov: list of the fixed covariates with which gene-environment
          interaction  will be considered.

   depen: =TRUE will use dependent prior for indicator variables of
          epistatic effects.

    prop: prior inclusion probabilities for epistatic effects in three
          different scenarios:  when none,one and both the main effects
          of the two interacting QTL are  included in the model. Note
          that the sum of the probabilities need not be equal to 1 and
          'prop' should be specified only when 'depen=TRUE'. 

     ...: Not used.

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

     This function defines the model for Bayesian QTL mapping using
     'qb.mcmc'. This model considers two-way interaction as the highest
     level of both gene-gene and gene-environment interactions.

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

qtl_envi: Indicates if there is an interaction between the QTLs and
          environmental variables: TRUE or FALSE.

_N_o_t_e:

     This function returns a list and hence should have a differenct
     name from that of the 'cross' object.

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

     Dr. Nengjun Yi, et al.,  nyi@ms.ssg.uab.edu

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

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

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

     'qb.data',  'qb.genoprob',   'qb.mcmc'

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

     qbModel <- qb.model(cross, chr.nqtl = rep(3,nchr(cross)), intcov = 1,
       interval = rep(10,3))  

