function to plot GWAA results

plot.scan.gwaa {GenABEL}R Documentation

function to plot GWAA results

Description

Plots results of GWA analysis

Usage

plot.scan.gwaa(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.

Author(s)

Yurii Aulchenko

See Also

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

Examples

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

[Package GenABEL version 1.6-7 Index]