plot.qb.loci             package:qtlbim             R Documentation

_J_i_t_t_e_r_e_d _p_l_o_t _o_f _B_a_y_e_s_i_a_n _Q_T_L _l_o_c_i _s_a_m_p_l_e_s _b_y _c_h_r_o_m_o_s_o_m_e

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

     Each point is one locus from the Bayesian QTL estimates, plotted
     vertically by chromosome, jittered to give a sense of density.
     Separate colored vertical bands by loci element.

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

     qb.loci(qbObject, loci = c("main", "epistasis", "GxE"), covar, ...)
     ## S3 method for class 'qb.loci':
     plot(x, loci, labels = FALSE, amount = 0.35, cex, col, ...)
     ## S3 method for class 'qb.loci':
     print(x, ...)
     ## S3 method for class 'qb.loci':
     summary(object, digit = 1, ...)

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

qbObject: Object of class 'qb'.

    loci: Character string identifying MCMC sample elements; may
          include '"main"', '"epistasis"', '"GxE"' and '"all"'.

   covar: Fixed covariate(s) for '"GxE"' loci; default is all fixed
          covariates involved in GxE interactions.

       x: Object of class 'qb.loci'.

  object: Object of class 'qb.loci'.

  labels: Include marker labels if TRUE.

  amount: Amount of 'jitter' (between 0 and .45)

     cex: Character expansion (may be invisible if too small-default
          based on number of MCMC samples).

     col: Character string with colors named by 'loci'; also includes
          color for 'marker' lines.

   digit: Number of digits for roundoff of loci quantiles.

     ...: Graphical parameters can be given as arguments to 'plot'. Not
          used in 'qb.loci'.

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

     Focuses attention on chromosome lengths and concentration of QTL
     loci estimates. Horizontal lines at markers. Separate bands by
     'loci' for each chromosome. Adjust 'amount' and 'cex' to modify
     look of plot. Most useful when looking at multiple chromosomes.

_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:

     'jitter','subset.qb'

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

     temp <- qb.loci(qbExample)
     plot(temp)
     summary(temp)
     temp <- qb.loci(qbExample, "all")
     plot(temp)
     summary(temp)

