Description Usage Arguments Value Examples
aGE interaction test
1 2 3 |
Y |
a numeric vector of phenotype values |
G |
a matrix for all RVs in the test gene or genomic region. The order of rows must match the order of Y. Missing is imputed as 0. |
cov |
a matrix with first column as the environmental variable to be tested. The order of rows must match the order of Y. |
model |
"binomial" for binary traits or "gaussian" for quantitative traits. |
pow |
Gamma set used to build a family of tests, default=c(1:6) for rare variants |
n.perm |
number of simulation to calculate the p-values, default=1000. Can increase to higher value depending on the signficiance level. |
method |
only have one option: "Simulation", also called Monte Carlo Method. |
nonparaE |
"T": use cubic splines for the environmental variable to fit the model; "F": use a linear function of the environmental variable to fit the model |
DF |
degree of freedom to use in the cubic splines, default=10. This option only works when nonparaE is set to "T" |
stepwise |
an option to speed up the simulation procedure for large n.perm number in real-data application. Up to $n.perm=10^8$ |
p-values
1 2 3 4 5 6 7 8 | {
set.seed(12345)
phenotype <- c(rep(1,50),rep(0,50))
genotype <- data.frame(g1=sample(c(rep(1,10),rep(0,90))),g2=sample(c(rep(1,5), rep(0,95))))
covariates <- data.frame(Envir=rnorm(100), Age=rnorm(100,60,5))
exD <- list(Y=phenotype, G=genotype, X=covariates)
aGE(Y=exD$Y, G=exD$G, cov=exD$X, model='binomial', nonparaE=FALSE, stepwise=FALSE)
}
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