prs.predict: Polygenic risk score; prediction

In sdzhao/ssa: Simultaneous Signal Analysis

Description

Polygenic risk score; prediction

Usage

prs.predict(newX, prs, P = NULL)

Arguments

newX	n x p matrix of additively coded genotypes to be predicted; IMPORTANT: must be coded relative to the same allele as in the cases and controls
prs	output of prs.train()
P	prevalence of cases in the testing set; if NULL, P is taken from the train object

Value

score	risk score
class	predicted class, 0=control, 1=case

Examples

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]));
## training data
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 <- prs.train(colMeans(X0)/2,colMeans(X1)/2,n0,n1);
## testing data
newX <- rbind(t(replicate(n0,rbinom(p,2,pi0))),
              t(replicate(n1,rbinom(p,2,pi1))));
newY <- c(rep(0,n0),rep(1,n1));
Yhat <- prs.predict(newX,prs);
mean(abs(newY-Yhat$class));

sdzhao/ssa documentation built on May 18, 2019, 2:36 p.m.