Find betas for risk haplotypes and intercept (beta for base.index haplotype) with a given r2
find.haplo.beta.qt(haplo, haplo.freq, base.index, haplo.risk, r2, y.mu=0, y.var=1)
find.beta.qt.phase.known(beta.size, haplo.risk, base.index, haplo,
haplo.freq, r2, y.mu, y.var)
find.intercept.qt.phase.known(beta.no.intercept, base.index, haplo, haplo.freq, y.mu)beta estimates for haplotypes or intercept
matrix of haplotypes, with rows the different haplotypes and columns the alleles of the haplotypes. For H haplotypes of L loci, haplo has dimension H x L.
vector of length H for the population haplotype frequencies (corresponding to the rows of haplo)
integer index of the haplotype considered to be the base-line for logistic regression (index between 1 and H); often, the most common haplotype is chosen for the base-line.
vector of relative risks for haplotypes
correlation coefficient
mean of y, a quantitative trait
variance of y, a quantitative trait
beta values for risk haplotypes in find.beta.qt.phase.known
beta vector for haplotypes for quantitative trait, excluding the beta for intercept