NAM (version 1.1.2)

Manhattan Plot: Plotting Genome-Wide Association Study

Description

Generates a Manhattan plot for a $gwas$ object.

Usage

manhattan(gwas, colA = 2, colB = 4, alpha=0.05, ...)

Arguments

gwas

An output of the function gwas.

colA

Color of even chromosomes.

colB

Color of odd chromosomes.

alpha

If specified, it provides the negative log p-value based on a chi squared distribution with a significance threshold for the given alpha.

...

Other arguments for plotting function.

Examples

data(tpod)
test=gwas(y=y,gen=gen[,1:240],fam=fam,chr=chr[1:12])
manhattan(gwas=test,colA=3,colB=1,type="h",lwd=2)
ii = 1+(2*test$PolyTest$lrt>4.9)
manhattan(gwas=test,pch=ii+3,lwd=ii)