QTLRel (version 1.14)

qtlVar: QTL Variance

Description

Estimate variance in a quantitative trait induced by QTL.

Usage

qtlVar(lrt, prdat, simulation = FALSE, nsim = 25)

Value

A vector displaying the estimated variance at each loci.

Arguments

lrt

A data frame (a, d, ...), where 'a' and 'd' are respectively additive and dominance effects.

prdat

A 3-D array that provides probabilities of genotypes "AA", "AB" and "BB". If prDat is an object of genoProb, then prdat can be prDat$pr.

simulation

Whether to use simulations to estimate the variance explained by QTL.

nsim

Number of simulations to perform if simulation is TRUE.

See Also

scanOne and genoProb

Examples

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])

gdtmp<- geno
   gdtmp<- replace(gdtmp,is.na(gdtmp),0)
# rung 'genoProb'
prDat<- genoProb(gdat=gdtmp, gmap=gmapF8,
   gr=8, method="Haldane", msg=TRUE)
# estimate variance components
o<- estVC(y=pheno$bwt, x=pheno$sex, v=v)

# genome scan
pv.hk<- scanOne(y=pheno$bwt, x=pheno$sex, prdat=prDat, vc=o)

# run 'qtlVar'
qef<- pv.hk$par[,c("a","d")]
   qef<- as.data.frame(qef)
qv<- qtlVar(qef,prDat$pr)
}