GenABEL (version 1.8-0)

plot.scan.gwaa.2D: function to plot 2D scan results

Description

Plots results of 2D analysis produced by scan.glm.2D or scan.haplo.2D

Usage

"plot"(x, y, ..., df=1)

Arguments

x

object of type scan.gwaa.2D-class, as returned by scan.glm.2D or scan.haplo.2D

y

this argument is not used

...

additional arguments to be passed to plot

df

Whether 1, 2, or "all" d.f.s should be plotted. Note that for scan.haplo.2D 1 and 2 d.f. list the same values.

Value

No value returned.

Details

Now plots only "allelelic" results. This is fine for scan.haplo.2Das only alleic tests are produced; however, scan.glm.2D also produces "genotypic" results.

See Also

scan.gwaa.2D-class, scan.glm.2D, scan.haplo.2D

Examples

require(GenABEL.data)
data(srdta)
a <- scan.glm.2D("qt3~CRSNP",data=srdta,snps=c(1:10))
# "allelic" results
plot(a)
# to plot "genotypic" results:
filled.contour(x=a$map,y=a$map,z=-log10(a$P2df))