NAM (version 1.0.2.2)

manhattan: Plotting Genome-Wide Association Study

Description

Generates a Manhattan plot for a $gwas$ object.

Usage

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

Arguments

gwas

An output of the function gwas.

colA

Color of even chromosomes.

colB

Color of odd chromosomes.

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)