qb.hpdone               package:qtlbim               R Documentation

_H_i_g_h_e_s_t _p_r_o_b_a_b_i_l_i_t_y _d_e_n_s_i_t_y (_H_P_D) _r_e_g_i_o_n.

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

     Determine HPD region across genome, including position of
     posterior mode.

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

     qb.hpdone(qbObject, level = 0.5, profile = "2logBF",
       effects = "cellmean", scan = "sum", chr, smooth = 3, ...)
     ## S3 method for class 'qb.hpdone':
     summary(object, chr, digits = 3, ...)
     ## S3 method for class 'qb.hpdone':
     print(x, ...)
     ## S3 method for class 'qb.hpdone':
     plot(x, chr, smooth = 3, ...)

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

qbObject: Object of class 'qb'.

  object: Object of class 'qb.hpdone'.

       x: Object of class 'qb.hpdone'.

   level: Value between 0 and 1 of HPD coverage.

    scan: Elements to scan; usually one of '"sum"', '"mean"',
          '"epistasis"', '"GxE"'.

  smooth: Degree of smoothing.

     chr: Chromosomes to include; default determined by HPD region.

 effects: Effects are '"cellmean"' for means by genotype; '"estimate"'
          for estimates of Cockerham main effects.

 profile: Objective profile for plot; default is '"2logBF"'; other
          choices found in option 'type' for 'qb.scanone'.

  digits: Number of digits for 'round'.

     ...: Extra parameters passed along to plot.

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

     Determine 100*'level' percent HPD region. Subset chromosomes based
     on HPD region. Create genome scans for 'profile' and 'effects'.

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

     'qb.hpdone' is a list with a 'hpd.region' summary matrix and
     'qb.scanone' objects for the 'profile' and 'effects'. A summary of
     a 'qb.hpdone' object yields a matrix with columns for 

     chr: chromosome number

   n.qtl: estimated number of QTL on chromosome

     pos: estimated position of QTL

  lo.nn%: lower nn% HPD limit

  hi.nn%: upper nn% HPD limit

 profile: Peak of profile, identifed by the profile type.

 effects: Columns for the effects, appropriately labeled.

_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:

     'qb.scanone'

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

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

