plot.scan.gwaa.2D: function to plot 2D scan results
In GenABEL: genome-wide SNP association analysis

Description Usage Arguments Details Value Author(s) See Also Examples

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

1 2	## S3 method for class 'scan.gwaa.2D' plot(x, y, ..., df=1)

`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.

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.

No value returned.

Yurii Aulchenko

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

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))