getSimulatedPhenotype: getSimulatedPhenotype

In AcceptABEL: A package for controlling false positives rate in GWAS by estimating local inflation factor

Description

Retrieve simulated phenotypes

Usage

getSimulatedPhenotype(data, snp.name, trait.name, covars = "")

Arguments

data
snp.name
trait.name
covars

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (data, snp.name, trait.name, covars = "") 
{
    variances <- c(1, 1, 1)
    snp.num <- which(snpnames(data) == snp.name)
    gtypes <- as.numeric(data@gtdata[, snp.num])
    means <- getMeans(data, snp.name, trait.name)
    if (sum(is.na(gtypes)) > 0) {
        warning("Missing genotypes found. Filling with the most frequent allele.")
        gtypes[is.na(gtypes)] <- 0
    }
    freqs <- as.vector(table(gtypes)/length(gtypes))
    phtypes <- rep(0, length(gtypes))
    phtypes[gtypes == 0] <- rnorm(length(gtypes[gtypes == 0]), 
        mean = means[1], sd = sqrt(variances[1]))
    phtypes[gtypes == 1] <- rnorm(length(gtypes[gtypes == 1]), 
        mean = means[2], sd = sqrt(variances[2]))
    phtypes[gtypes == 2] <- rnorm(length(gtypes[gtypes == 2]), 
        mean = means[3], sd = sqrt(variances[3]))
    H2 <- getH2(data, snp.name, trait.name, covars)
    phtypes <- phtypes + getError(H2, freqs, means, length(phtypes))
    phtypes
  }

AcceptABEL documentation built on May 2, 2019, 5:24 p.m.