RNOmni (version 1.0.0)

IINT: Indirect-INT

Description

Two-stage association testing procedure. In the first stage, phenotype y and genotype G are each regressed on the model matrix X to obtain residuals. The phenotypic residuals are transformed using RankNorm. In the next stage, the INT-transformed residuals are regressed on the genotypic residuals.

Usage

IINT(y, G, X = NULL, k = 0.375, simple = FALSE)

Value

If simple = TRUE, returns a vector of p-values, one for each column of G. If simple = FALSE, returns a numeric matrix, including the Wald or Score statistic, its standard error, the Z-score, and the p-value.

Arguments

y

Numeric phenotype vector.

G

Genotype matrix with observations as rows, SNPs as columns.

X

Model matrix of covariates and structure adjustments. Should include an intercept. Omit to perform marginal tests of association.

k

Offset applied during rank-normalization. See RankNorm.

simple

Return the p-values only?

See Also

• Basic association test BAT.

• Direct INT test DINT.

• Omnibus INT test OINT.

Examples

set.seed(100)
# Design matrix
X <- cbind(1, rnorm(1e3))
# Genotypes
G <- replicate(1e3, rbinom(n = 1e3, size = 2, prob = 0.25))
storage.mode(G) <- "numeric"
# Phenotype
y <- exp(as.numeric(X %*% c(1,1)) + rnorm(1e3))
# Association test
p <- IINT(y = y, G = G, X = X)