find.haplo.beta.qt: Find beta coefficients for risk haplotypes, for specified r2

In haplo.stats: Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

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

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

haplo.stats documentation built on May 29, 2024, 9:53 a.m.