powerGcE: powerGcE

In SharonLutz/powerGcE: runs the powerGcE function

powerGcE

Description

Evaluate gene by environment interaction with a binary outcome and a normally distributed environmental exposure.

Usage

powerGcE(nCase = 407, nControl = 376, MAF = 0.49, meanE = 0, varE = 0.99, beta0 = -0.32, betaSNP = 0.17, betaE = 0.97, betaI = seq(-1, -0.75, by = 0.05), nSim = 1000, alpha = 5e-08, plot.output = TRUE, plot.name = "powerGcE.pdf", seed = 1)

Arguments

nCase	is the number of cases
nControl	is the number of controls
MAF	is the minor allele frequency for the SNP
meanE	is the mean of the normally distributed environmental exposure
varE	is the variance of the normally distributed environmental exposure
beta0	For the binary outcome Y, the environmental exposure E, and the SNP, logit(P(Y=1))=Beta0+BetaSNP*SNP+BetaE*E+BetaI*SNP*E
betaSNP	For the binary outcome Y, the environmental exposure E, and the SNP, logit(P(Y=1))=Beta0+BetaSNP*SNP+BetaE*E+BetaI*SNP*E
betaE	For the binary outcome Y, the environmental exposure E, and the SNP, logit(P(Y=1))=Beta0+BetaSNP*SNP+BetaE*E+BetaI*SNP*E
betaI	For the binary outcome Y, the environmental exposure E, and the SNP, logit(P(Y=1))=Beta0+BetaSNP*SNP+BetaE*E+BetaI*SNP*E
nSim	is the number of simulations
alpha	is the alpha level, default=0.00000005
plot.output	if true, then a plot is outputted to the working directory.
plot.name	is the name of the plot.
seed	is set for reproducibility.

Value

The SNP is generated from a binomial distribution and the environmental exposure from a normal distribution. Then, the binary outcome is generated from a binomial distribution such that logit(P(Y=1))=Beta0+BetaSNP*SNP+BetaE*E+BetaI*SNP*E where E is the environmental exposure. We exmained the proportion of simulations where the p-value for the interaction term is less than alpha.

Author(s)

Sharon Lutz

Examples

	powerGcE(nCase = 407, nControl = 376, MAF = 0.49, meanE = 0, varE = 0.99, beta0 = -0.32, betaSNP = 0.17, betaE = 0.97, betaI = seq(-1, -0.75, by = 0.05), nSim = 1000, alpha = 5e-08, plot.output = TRUE, plot.name = "GcE.pdf", seed = 1)

SharonLutz/powerGcE documentation built on Nov. 22, 2024, 4:21 p.m.