man_plot_pvalue: Create Manhattan plot for pvalue based models

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

Description

Create Manhattan plot for pvalue based models

Usage

man_plot_pvalue(ba, type = c("SNP", "Win"), col = c("black", "red"),
  ylim = c(0, 12), ...)

Arguments

ba	an object of the class ba generated by baFit
type	can be c("SNP","Win") for single SNP or window based Manhattan plot
col	color for the Manhattan plot
ylim	the range of yaxis
...	other plot options

Value

Null. This function only prints to the screen.

Examples

## Not run: 
 rm(list=ls())
 library(BATools)
 data("Pig")
 #Standardize genotype matrix
 run_para=list(maxiter=100)
 update_para=list(df=FALSE,scale=TRUE,pi=FALSE)
 op<-create.options(model="GBLUP",method="REML",priors=NULL,init=init,
                  update_para=update_para,run_para=run_para,save.at="GBLUP",print_mcmc=NULL)
 gblup<-baFit(driploss~sex,data=PigPheno,geno=geno ,genoid = ~id,options = op,map=PigMap,GWA="SNP")
 par(mfrow=c(1,2))
 man_plot_pvalue(gblup)
 man_plot_pvalue(gblup,type="Win")

## End(Not run)

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