plot.check.marker: plots "check.marker" object
In GenABEL: genome-wide SNP association analysis

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

Plots "check.marker" object, as returned by check.marker

1 2	## S3 method for class 'check.marker' plot(x, y, ...)

`x`	Object of class "check.marker", as returned by `check.marker` or `snp.subset`
`y`	this argument is not used
`...`	other arguments to be passed to plot

In this plot, along the X axes, you can see colour representation of markers which did not pass (pass – black) the QC. The diagonal shows redundant markers. If for some marker there exist markers, which show exactly the same (or some minimum concordance) genotypic distribution, such markers are depicted as crosses an solid line is dropped on the X axes from it. Other solid line connects the original SNP with the redundant ones (depicted as circles). From each redundant SNP, a dashed line is dropped on X. Normally, one expects that redundant markers are positioned very closely and redundancy appears because of linkage disequilibrium.

No value returned. Explanatory note is shown on the screen.

Yurii Aulchenko

check.marker, snp.subset

require(GenABEL.data)
data(srdta)
mc <- check.marker(data=srdta@gtdata[,1:100],redundant="all",maf=0.01,
					minconcordance=0.9,fdr=.1,ibs.mrk=0)
mc <- check.marker(data=srdta@gtdata[,1:100],maf=0.01,fdr=.1,ibs.mrk=0)
plot(mc)
mc1 <- snp.subset(mc,snps=srdta@gtdata@snpnames[20:40])
plot(mc1)