check.marker-class: Class "check.marker"
In GenABEL: genome-wide SNP association analysis

Description Names Methods Author(s) See Also Examples

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

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

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

Yurii Aulchenko

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

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)