SNPassoc

library(SNPassoc)
data(SNPs)

### Bonferroni.sig
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=F)

### SNPs.info.pos
data(SNPs.info.pos)
SNPs.info.pos

### Table.N.Per
Table.N.Per(SNPs$snp10001, SNPs$casco)
Table.N.Per(SNPs$snp10001, SNPs$casco, SNPs$sex=="Male")
Table.N.Per(dominant(snp(SNPs$snp10001,sep="")), SNPs$casco)

### Table.mean.se
Table.mean.se(SNPs$snp10001, SNPs$protein)
Table.mean.se(SNPs$snp10001, SNPs$protein, SNPs$sex=="Male")
Table.mean.se(dominant(snp(SNPs$snp10001,sep="")), SNPs$protein, SNPs$sex=="Male")
#tapply(SNPs$protein, SNPs$snp10001, mean)

### model = c("codominant", "dominant", "recessive", "overdominant", "log-additive", "all")
ansCoAd <- WGassociation(protein~1, data=datSNP, model=c("codominant","log-add"))
plot(ansCoAd)
summary(ansCoAd)