plot.qb.epistasis           package:qtlbim           R Documentation

_D_e_n_s_i_t_y _P_l_o_t_s _f_o_r _M_o_d_e_l_s _S_h_o_w_i_n_g _E_p_i_s_t_a_s_i_s _a_n_d _G_x_E _I_n_t_e_r_a_c_t_i_o_n_s.

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

     Produces density plots of models showing epsistasis
     ('qb.epistasis') or GxE interactions ('qb.intcov'). The vertical
     axis shows magnitude of effect, horizontal axis shows chromosomes
     in epistatic pairs or covariate by chromosome.  Paralell plots are
     produced for each of the entries in the 'effects' parameter.

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

     qb.epistasis(qbObject, effects = c("aa", "ad", "da", "dd"),
       cutoff = 1, maxpair = 5, pairs, ...)
     qb.intcov(qbObject, covar, effects = c("add","dom"),
       cutoff = 1, nmax = 5, cov.chr, ...)
     ## S3 method for class 'qb.epistasis':
     plot(x, effects, cex = 0.5, main, ... )
     ## S3 method for class 'qb.epistasis':
     print(x, ... )
     ## S3 method for class 'qb.epistasis':
     summary(object, ... )

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

qbObject: An object of class 'qb'.

  object: Object of class 'qb.epistasis'.

       x: Object of class 'qb.epistasis'.

  cutoff: The 'cutoff' parameter for number of epistatic pairs.

 maxpair: Maximum number of epistatic pairs shown.

   pairs: A character vector of chromosome pairs to examing for
          epistatic pairs.  Chromosome names are separated by a dot.

   covar: Covariate(s) to include; default is 'seq(nfixcov)' where
          'nfixcov' is taken from 'qb.data'.

    nmax: Maximum number of covariate chromosomes shown.

 cov.chr: A character vector of covariate by chromosome pairs to
          examing for GxE effects.  Covariate names and chromosome
          names are separated by a dot.

 effects: Character string of model effects.

     cex: Horizontal expansion factor for characters in the plot. See
          'par'.

    main: Main titles for plots; default is 'effects'.

     ...: Arguments passed to generic 'plot'.

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

     Returns a table of counts of epistatic pairs with counts above the
     cutoff value.

_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>

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

     temp <- qb.epistasis(qbExample)
     summary(temp)
     plot(temp)
     temp <- qb.intcov(qbExample)
     summary(temp)
     plot(temp)

