GenomicControl: Population substructure

In SNPassoc: SNPs-Based Whole Genome Association Studies

Population substructure

Description

This function estimates an inflation (or deflation) factor, lambda, as indicated in the paper by Devlin et al. (2001) and corrects the p-values using this factor.

Usage

GenomicControl(x, snp.sel)

Arguments

x	an object of class 'WGassociation'.
snp.sel	SNPs used to compute lambda. Not required.

Details

This method is only valid for 2x2 tables. This means that the object of class 'WGassociation' might not have fitted the codominant model.

See reference for further details.

Value

The same object of class 'WGassociation' where the p-values have been corrected for genomic control.

References

B Devlin, K Roeder, and S.A. Bacanu. Unbiased Methods for Population Based Association Studies. Genetic Epidemiology (2001) 21:273-84

See Also

qqpval, WGassociation

Examples

data(SNPs) 
datSNP<-setupSNP(SNPs,6:40,sep="")
res<-WGassociation(casco,datSNP,model=c("do","re","log-add"))

# Genomic Control 
resCorrected<-GenomicControl(res)

SNPassoc documentation built on Dec. 28, 2022, 1:59 a.m.