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 1.3-7
Index]