NAM (version 1.7.3)

Manhattan: Manhattan plot for Association Studies

Description

Generates a graphical visualization for the output of the function gwas/gwas2/gwasGE.

Usage

# S3 method for NAM
plot(x,...,alpha=0.05,colA=2,colB=4,find=NULL,FDR=NULL,gtz=FALSE,phys=NULL)

Arguments

x

Output of the gwas/gwas2/gwas3 function.

...

Further arguments passed to or from other methods.

alpha

Numberic. Significance threshold to display in the Manhattan plot.

colA

Color of odd chromosomes in the Manhattan plot.

colB

Color of even chromosomes in the Manhattan plot.

find

Integer. If provided, you can click on the specified number of hits in the Manhattan plot to obtain the name of the markers.

FDR

Null or numeric between zero and one. If provided, it will display the Manhattan plot with Bonferroni threshold by chromosome, adjusted for the specified false discovery rate (FDR). Thus, zero provides the Bonferroni correction.

gtz

Logical. If TRUE, the argument FDR will just take into account markers with p-value Greater Than Zero (GTZ).

phys

Numeric vector with length equal to the number of markers. If provided, the Manhattan plot is generated using the physical distance in the x axis.

Examples

# NOT RUN {
data(tpod)
test=gwas2(y=y,gen=gen[,1:240],fam=fam,chr=chr[1:12])
par(mfrow=c(2,1))

# Example Manhattan 1
SIGNIF = 1+(2*test$PolyTest$lrt>4.9)
plot(x=test,pch=SIGNIF+3,lwd=SIGNIF,main="Example 2")

# Example Manhattan 2
plot(x=test,main="Example 3",pch=20,lwd=2)
Kern = ksmooth(1:240,test$PolyTest$lrt,bandwidth=1)
lines(Kern,type="l",lwd=2)
# }