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
Examples
data(SNPs)
datSNP<-setupSNP(SNPs,6:40,sep="")
res<-WGassociation(casco,datSNP,model=c("do","re","log-add"))
# Genomic Control
resCorrected<-GenomicControl(res)
[Package SNPassoc version 2.1-0 Index]