calcBaselineLOddsFromSample {mgrp}R Documentation

Calculate Baseline Log-Odds required for a desired disease prevalence given a sample of genotypes, and a genotype profile specifying the risk allele frequencies and the disease odds ratios (see calcBaselineLOdds).

Description

Calculates the baseline log-odds for a genotype in order to achieve the desired disease prevalence (expected risk). The function takes a disease prevalence(p) and vectors for each of odds ratio("or"), frequency of risk allele in the population("f") and number of genes ("nog"). The genotype will then consist of nog[i] genes each with f[i] risk allele frequency and or[i] disease odds ratio for each instance of the risk allele. (the overall genotype will be made up of of sum(nog) genes.

To calculate a baseline log odds, three assumptions are made:
(1) Each version of the allele is assumed to give the same increased risk for disease, such that OR for homozygote with the risk allele (compared to the homozygote non-risk allele) is $or^2$ (where "or" is the odds ratio for a heterozygote relative to the homozygote non-risk allele).
(2) The alleles are assumed to be in Hardy-Weinberg equilibrium such that the overall allele frequency fully specifies the frequencies of each of EE,Ee,ee.
(3) The log odds ratios are additive, and there is no interaction between genes in the genotype.
Once we fix or, f and p we can solve for a unique baseline log odds which will yield the desired prevalence of disease in the population. Overall risk for a given genotype is then expit(sum #riskalleles[i] * or[i] + log baseline odds).

Usage

calcBaselineLOddsFromSample(or,f,nog,p,sampGenotypes)

Arguments

or (A vector of) disease odds ratio(s) for the heterozygote relative to the homozygote non-risk allele.
f A vector of) frequency of the risk allele in the population
nog A vector of) number of genes for each f/or combination
p The prevalence of the disease in the population
sampGenotypes A sample of genotypes for a population.

Value

calcLR returns a list:

or The input disease odds ratio for the heterozygote
f The input frequency of the risk allele
p The input prevalence of the disease in the population
nog The input numbers of genes in the population
bLO The baseline log odds to achieve the desired prevalence.

Author(s)

Daryl Morris

Examples

sampleGenes <- function(ff,nn) {
  sapply(ff,function(x) sample(1:3,nn,replace=TRUE,
         prob=c(x^2,2*x*(1-x),(1-x)^2)))
}   

f <- seq(.4,.1,length.out=50)
or <- seq(1.5,1,length.out=50)
nog <- rep(1,50)
sample <- 10000
sampGenotypes  <- sampleGenes(f,sample)

calcBaselineLOddsFromSample(or=or,f=f,nog=nog,p=.05,sampGenotypes)

[Package mgrp version 1.0 Index]