R: 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

    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)

[Package GenABEL version 1.8-0 Index]