R: Find beta coefficients for risk haplotypes, for specified r2

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

[Package haplo.stats version 1.7.9 Index]