qb.arch                package:qtlbim                R Documentation

_B_u_i_l_d _g_e_n_e_t_i_c _a_r_c_h_i_t_e_c_t_u_r_e _w_i_t_h _c_h_r_o_m_o_s_o_m_e_s, _p_o_s_i_t_i_o_n_s _a_n_d
_e_p_i_s_t_a_t_i_c _p_a_i_r_s.

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

     These routines work in conjunction with 'qb.hpdone', 'qb.scantwo',
     'qb.sliceone' and 'step.fitqtl' to infer the number, pattern and
     position of QTL from MCMC samples.

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

     qb.arch(object, ...)
     ## Default S3 method:
     qb.arch(object, chr, pos, tolerance = 10, ...)
     ## S3 method for class 'step.fitqtl':
     qb.arch(object, main, epistasis, ...)
     ## S3 method for class 'qb.arch':
     summary(object, ...)
     ## S3 method for class 'qb.arch':
     print(x, ...)

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

  object: Object for appropriate method: summary of object of class
          'qb.scantwo' for default; object of class 'step.fitqtl'.

       x: Object of class 'qb.arch'.

     chr: Vector of chromosome numbers.

     pos: Vector of positions on chromosomes (much be same length as
          'chr').

tolerance: Minimum distance for two QTL to be considered distinct.

    main: Vector of chromosome identifiers with only main effects.

epistasis: Data frame with a 2-element vector of chromosome identifiers
          for each epistatic pair.

     ...: Not used here.

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

     Extract architecture in terms of chromosomes and positions of main
     QTL and identifiers of epistatic pairs of QTL. The 'step.fitqtl'
     approach is used to compare an automatic fit to a user-defined set
     of main chromosomes and epistatic pairs.

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

     qtl: Data frame with main QTL as 'chr' and 'pos'.

  by.num: Data frame with epistatic pairs indexed by chromosome number,
          labeled 'qtla' and 'qtlb'.

  by.chr: List with elements 'chr' and 'pos' showing epistatic pairs.
          These elements are data frames with chromosomes and positions
          for each epistatic pair: rows are QTL number, columns are
          'qtla' and 'qtlb'.

  by.set: List of connected sets of epistatic chromosomes.

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

     Brian S. Yandell

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

     http://www.qtlbim.org

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

     'step.fitqtl', 'qb.sweave'

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

     ## Run qb.scantwo and get summary to use in qb.arch
     temp <- summary(qb.scantwo(qbExample, type = "2logBF"),
       threshold = c(upper = 10))
     ## qb.arch default use. 
     cross.arch <- qb.arch(temp, chr = c(1,1,2,3), pos = c(15,45,12,15))
     cross.arch

