prs.train: Polygenic risk score (given only allele frequencies);...
In ssa: Simultaneous Signal Analysis

Description Usage Arguments Value Examples

Equivalent to maximum likelihood naive Bayes classifier. The discriminant function is

∑_j\hat{β}_jX_j,

where X_j is the additively coded genotype of SNP j.

1	prs.train(pi0, pi1, n0, n1)

`pi0, pi1`	p x 1 vectors of control and case minor allele frequencies, respectively; IMPORTANT: must be relative to the same allele in both cases and controls
`n0, n1`	number of controls and number of cases, respectively

`pi0`	minor allele frequencies in controls
`pi1`	minor allele frequencies in cases
`P`	proportion of cases

p <- 1000; ## number of snps
I <- rep(0,p); I[1:10] <- 1; ## which snps are causal
set.seed(1); pi0 <- runif(p,0.1,0.5); ## control minor allele frequencies
set.seed(1); ors <- runif(sum(I),-1,1); ## odds ratios
pi1 <- pi0;
pi1[I==1] <- expit(ors+logit(pi0[I==1]));
n0 <- 100; ## number of controls
X0 <- t(replicate(n0,rbinom(p,2,pi0))); ## controls
n1 <- 50; ## number of cases
X1 <- t(replicate(n1,rbinom(p,2,pi1))); ## cases
prs.train(colMeans(X0)/2,colMeans(X1)/2,n0,n1);