NAM (version 1.1.2)

manhattan: Plotting Genome-Wide Association Study

Description

Generates a Manhattan plot for a $gwas$ object.

Usage

manhattan(gwas, colA = 2, colB = 4, alpha=NULL, GenDist = FALSE, OtherDist = NULL, ...)

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.

GenDist

Logical. If true, it displays the Manhattan plot with the estimated genetic map for NAM populations.

OtherDist

Numeric vector of length ($m$), equal to the number of columns in $gen$. If provided, it changes the X coordinates used for the Manhattan plot.

...

Other arguments for plotting function.

Examples

data(tpod)
test=gwas(y=y,gen=gen,fam=fam,chr=chr)
manhattan(gwas=test,colA=3,colB=1,type="h",lwd=2)
manhattan(gwas=test,GenDist=TRUE,pch=20)