R: Population substructure

GenomicControl {SNPassoc} | R Documentation

## 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)
    plot(resCorrected)

[Package SNPassoc version 1.9-2 Index]