baplot: plot result for baFit

In chenchunyu88/BATools: BATools: An R package that extends 'Bayesian Alphabet' for Whole Genome Prediction and Genome-wide association study

Description

Plot the results for the Bayesian models

Usage

baplot(BAout = NULL, type = c("pre", "trace"), op = NULL,
  iterStart = NULL, col = c("black", "red"), ...)

Arguments

BAout	ba object contains all the output of the Bayesian model
type	string defines the type of the plot, which can be "pre","trace" "pre" plot the predicted value against the true value "trace" Traceplot
op	op object created by 'create.options' that is used for the analysis
iterStart	the starting iteration for traceplot
col	color for the plot in cross-validation

Examples

## Not run: 
 rm(list=ls())
 library(BATools)
 data("Pig")
 #Standardize genotype matrix
 #or set your own starting values using 
 #init=list(df=5,scale=0.01,pi=1) 
 run_para=list(niter=2000,burnIn=1000,skip=10)
 print_mcmc=list(piter=500)
 update_para=list(df=FALSE,scale=TRUE,pi=F)
 op<-create.options(model="SSVS",method="MCMC",seed=1,priors=NULL,init=init,
                  update_para=update_para,run_para=run_para,save.at="SSVS",print_mcmc=print_mcmc)
 #### Cross-validation using BATools
 set.seed(1234)
 PigPheno=createCV(data = PigPheno,k=5,"driploss")
 cvSSVS<-baFit(driploss~sex,data=PigPheno,geno=geno ,genoid = ~id,options = op, train=~cv1)
 par(mfrow=c(1,1))
 plot(cvSSVS)

## End(Not run)

chenchunyu88/BATools documentation built on May 19, 2019, 8:21 a.m.