Class "check.marker"

check.marker-class {GenABEL}R Documentation

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

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)

[Package GenABEL version 1.6-7 Index]