data(miscEx)
if (FALSE) {
# impute missing genotypes
pheno<- pdatF8[!is.na(pdatF8$bwt) & !is.na(pdatF8$sex),]
ii<- match(rownames(pheno), rownames(gdatF8))
geno<- gdatF8[ii,]
ii<- match(rownames(pheno), rownames(gmF8$AA))
v<- list(A=gmF8$AA[ii,ii], D=gmF8$DD[ii,ii])
# estimate variance components
o<- estVC(y=pheno$bwt, x=pheno$sex, v=v)
# impute missing genotypes
gdtmp<- genoImpute(geno, gmap=gmapF8, gr=8, na.str=NA, msg=FALSE)
# genome scan and plotting
lrt<- scanOne(y=pheno$bwt, x=pheno$sex, gdat=gdtmp, vc=o)
lrt
plot(lrt,gmap=gmapF8)
# Haley-Knott method
gdtmp<- geno; unique(unlist(gdtmp))
gdtmp<- replace(gdtmp,is.na(gdtmp),0)
prDat<- genoProb(gdat=gdtmp, gmap=gmapF8, gr=8, method="Haldane", msg=TRUE)
pv.hk<- scanOne(y=pheno$bwt, intc=pheno$sex, prdat=prDat, vc=o, test="F")
pv.hk
plot(pv.hk, gmap=gmapF8)
# assume additive allelic effects
class(prDat)<- c(class(prDat), "addEff")
lrt.hk<- scanOne(y=pheno$bwt, intc=pheno$sex, prdat=prDat, vc=o)
lrt.hk
}
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