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 1.4-2
Index]