qtlVar: QTL Variance

In QTLRel: Tools for Mapping of Quantitative Traits of Genetically Related Individuals and Calculating Identity Coefficients from Pedigrees

QTL Variance

Description

Estimate variance in a quantitative trait induced by QTL.

Usage

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

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.

Value

A vector displaying the estimated variance at each loci.

Note

Correlations among observations are ignored, and this function should be used with caution.

See Also

scanOne and genoProb

Examples

data(miscEx)

## Not run: 
# 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)

## End(Not run)

QTLRel documentation built on Aug. 9, 2023, 1:07 a.m.