| 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
snpokMarkers which passed all criteria
idokPeople which passed all criteria
nohweMarkers which did not pass HWE check
Pex.nohweExact HWE P-values for markers which did not pass HWE check
nocallMarkers with call rate < specified callrate
nofreqMarkers with MAF < specified maf
XmrkfailX-linked markers with too many heterozygous male genotypes
redundantRedundant markers
details.redundancyList with details on redundant markers (reference-marker <-> redundant-markers)
idnocallPeople with too low SNP call rate across al SNPs
hetfailPeople having too high heterozygosity
ibsfailPeople having too high IBS with other people
XidfailMen with too many heterozygous X-linked markers
callList 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 1.4-0
Index]