qb.covar               package:qtlbim               R Documentation

_E_x_a_m_i_n_e _G_x_E _e_f_f_e_c_t _o_f _c_o_v_a_r_i_a_t_e_s _o_n _m_a_i_n _g_e_n_e_t_i_c _e_f_f_e_c_t_s.

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

     Compare main effects with GxE effects to address correlation of
     estimates.

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

     qb.covar(qbObject, element = "add", covar = 1, adjust.covar, chr, ...)
     ## S3 method for class 'qb.covar':
     summary(object, percent = 5, digits = 3, ...)
     ## S3 method for class 'qb.covar':
     print(x, ...)
     ## S3 method for class 'qb.covar':
     plot(x, percent = 5, cex, include.zero = TRUE, ...)

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

qbObject: Object of class 'qb'.

  object: Object of class 'qb.covar'.

       x: Object of class 'qb.covar'.

 element: Main effect to examine ("add" or "dom").

   covar: Index to covariates used in MCMC samples.

adjust.covar: Adjustments to covariates. Default is 'NA', which adjusts
          by covariate mean values. Values are assumed to be in order
          of fixed covariates.

     chr: Subset of chromosomes as integer vector.

 percent: Percentile (0 to 100) for summaries.

  digits: Number of significant digits to print.

     cex: Character expansion for plots (default decreases with MCMC
          sample size).

include.zero: Include zero values in plot when 'TRUE'.

     ...: Arguments passed through to inherited routines.

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

     The diagonal dark green line of points on plots by chromosome
     indicate adjustment for covariates that have not been centered.
     Main effects are generally less correlated with GxE when
     covariates are first centered to have mean zero.

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

     Objects of class 'qb.covar' have three columns: main effect, GxE
     effect and chromosome. Summary objects have eight columns, three
     for main effect and GxE (mean, lower and upper percentile),
     followed by correlation and p-value. Summaries are done by
     chromosome.

_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.mcmc'

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

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

