GenABEL (version 1.8-0)

plot.scan.gwaa: function to plot GWAA results

Description

Plots results of GWA analysis

Usage

"plot"(x, y, ..., df=1, ystart=0, col=c("blue","green"), 
		sort=TRUE, ylim, delta = 1 , main = getcall(x))

Arguments

x

object of type scan.gwaa-class, as returned by scan.glm, qtscore, ccfast, emp.ccfast, emp.qtscore, or scan.haplo

y

this argument is not used

...

additional arguments to be passed to plot

df

Plot results of 1 or 2-df test (1, 2). Could be also "Pc1df" (for GC corrected P-values) and "Pc2df" (for robust genomic control of the 2 df test)

ystart

truncate lower value of Y at this point (can help avoiding plotting too may points)

ylim

ylim, same as in the standard plot function

col

which colors to use to depict consecutive chromosomes

sort

whether results should be plotted after sorting by chromosome and position

delta

gap width between chromosomes

main

title of the plot

Value

No value returned.

See Also

scan.gwaa-class, add.plot, snp.subset, scan.glm, qtscore, ccfast, emp.qtscore, emp.ccfast, scan.haplo

Examples

require(GenABEL.data)
data(srdta)
a <- qtscore(bt,srdta,snps=c(1:250))
plot(a)
add.plot(a,df="Pc1df",col="green")