Find beta coefficients for risk haplotypes, for specified r2

Description

Find betas for risk haplotypes and intercept (beta for base.index haplotype) with a given r2

Usage

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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)

Arguments

haplo

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.

haplo.freq

vector of length H for the population haplotype frequencies (corresponding to the rows of haplo)

base.index

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.

haplo.risk

vector of relative risks for haplotypes

r2

correlation coefficient

y.mu

mean of y, a quantitative trait

y.var

variance of y, a quantitative trait

beta.size

beta values for risk haplotypes in find.beta.qt.phase.known

beta.no.intercept

beta vector for haplotypes for quantitative trait, excluding the beta for intercept

Value

beta estimates for haplotypes or intercept

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