Manhattan: Manhattan plot for Association Studies

In alenxav/NAM: Nested Association Mapping

Description

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

Usage

## S3 method for class '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.

Author(s)

Alencar Xavier and William Beavis

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)

## End(Not run)

alenxav/NAM documentation built on Jan. 8, 2020, 9:21 p.m.