Class "check.marker"

Description

This class contains results of genotypic quality control. This is an list object, usually generated by check.marker.

Names

snpok

Markers which passed all criteria

idok

People which passed all criteria

nohwe

Markers which did not pass HWE check

Pex.nohwe

Exact HWE P-values for markers which did not pass HWE check

nocall

Markers with call rate < specified callrate

nofreq

Markers with MAF < specified maf

Xmrkfail

X-linked markers with too many heterozygous male genotypes

redundant

Redundant markers

details.redundancy

List with details on redundant markers (reference-marker <-> redundant-markers)

idnocall

People with too low SNP call rate across al SNPs

hetfail

People having too high heterozygosity

ibsfail

People having too high IBS with other people

Xidfail

Men with too many heterozygous X-linked markers

call

List with details on call: call, name (of marker), map, chromosome

Methods

summary

signature(object = "check.marker"): gives a cross table summrising how many markers did not pass because of this or that criteria

plot

signature(object = "check.marker"): Plots summary of genotypic data QC

Author(s)

Yurii Aulchenko

See Also

check.marker, summary.check.marker, redundant, plot.check.marker

Examples

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)
class(mc)
names(mc)
names(mc$call)
mc$nohwe
mc$Pex.nohwe
summary(mc)
plot(mc)