diff --git a/src/1.JWAS/src/MCMC/DRY.jl b/src/1.JWAS/src/MCMC/DRY.jl index d3b8c1a2..1649fea3 100644 --- a/src/1.JWAS/src/MCMC/DRY.jl +++ b/src/1.JWAS/src/MCMC/DRY.jl @@ -41,6 +41,8 @@ function errors_args(mme,methods) error("GBLUP runs with genotypes.") elseif mme.M.genetic_variance == false error("Please provide values for the genetic variance for GBLUP analysis") + elseif estimatePi == true + error("GBLUP runs with estimatePi = false.") end end if mme.nModels > 1 && mme.M!=0 diff --git a/src/1.JWAS/src/MCMC/MCMC.jl b/src/1.JWAS/src/MCMC/MCMC.jl index 1e0bb588..f1b6ceb2 100644 --- a/src/1.JWAS/src/MCMC/MCMC.jl +++ b/src/1.JWAS/src/MCMC/MCMC.jl @@ -150,8 +150,7 @@ function runMCMC(mme::MME,df; sol = starting_value, outFreq = printout_frequency, output_samples_frequency = output_samples_frequency, - output_file = output_samples_file, - update_priors_frequency = update_priors_frequency) + output_file = output_samples_file) else error("No options!!!") end diff --git a/src/1.JWAS/src/MCMC/MCMC_GBLUP.jl b/src/1.JWAS/src/MCMC/MCMC_GBLUP.jl index 9623b4a8..066e429e 100644 --- a/src/1.JWAS/src/MCMC/MCMC_GBLUP.jl +++ b/src/1.JWAS/src/MCMC/MCMC_GBLUP.jl @@ -54,7 +54,7 @@ function MCMC_GBLUP(nIter,mme,df; D = eigenG.values#eigenvalues dfEffectVar = mme.df.marker #actually for genetic effect here - vEff = mme.M.G #genetic variance + vEff = mme.M.genetic_variance #genetic variance scaleVar = vEff*(dfEffectVar-2)/dfEffectVar #scale factor for locus effects meanVara = 0.0 meanVarg = 0.0 @@ -104,7 +104,6 @@ function MCMC_GBLUP(nIter,mme,df; if iter > burnin meanAlpha += (α - meanAlpha)/(iter-burnin) end - ######################################################################## # 2.1 Genetic Covariance Matrix (Polygenic Effects) (variance.jl) ######################################################################## @@ -158,7 +157,7 @@ function MCMC_GBLUP(nIter,mme,df; println("\nPosterior means at iteration: ",iter) println("Residual variance: ",round(meanVare,digits=6)) if mme.pedTrmVec !=0 - println("Polygenic effects covariance matrix \n",round(G0Mean,digits=3)) + println("Polygenic effects covariance matrix \n",round.(G0Mean,digits=3)) end println("Genetic variance (G matrix): ",round(meanVara,digits=6)) println("Genetic variance (GenSel): ",round(meanVarg,digits=6))