find.haplo.beta.qt {haplo.stats}R Documentation

Find beta's for risk haplotypes, for specified r2

Description

Find intercept (beta for base.index haplotype)

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

[Package haplo.stats version 1.3.8 Index]