Usage
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