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

View source: R/find.haplo.beta.qt.q

find.haplo.beta.qtR Documentation

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 Jan. 22, 2023, 1:40 a.m.