Bonferroni.sig: Bonferroni correction of p values

Description

This function shows the SNPs that are statistically significant after correcting for the number of tests performed (Bonferroni correction) for an object of class "WGassociation"

Usage

Bonferroni.sig(x, model = "codominant", alpha = 0.05, 
      include.all.SNPs=FALSE)

Arguments

an object of class 'WGassociation'.

model

a character string specifying the type of genetic model (mode of inheritance). This indicantes how the genotypes should be collapsed when 'plot.summary' is TRUE. Possible values are "codominant", "dominant", "recessive", "overdomi

alpha

nominal level of significance. Default is 0.05

include.all.SNPs

logical value indicating whether all SNPs are considered in the Bonferroni correction. That is, the number of performed tests is equal to the number of SNPs or equal to the number of SNPs where a p value may be computed. The default value is FAL

Value

A data frame with the SNPs and the p values for those SNPs that are statistically significant after Bonferroni correction

Details

After deciding the genetic model, the function shows the SNPs that are statistically significant at alpha level corrected by the number of performed tests.

Examples

Run this code

data(SNPs)
datSNP<-setupSNP(SNPs,6:40,sep="")
ans<-WGassociation(protein~1,data=datSNP,model="all")
Bonferroni.sig(ans, model="codominant", alpha=0.05, include.all.SNPs=FALSE)