IINT: Indirect-INT

In RNOmni: Rank Normal Transformation Omnibus Test

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, ties.method = "average", simple = FALSE)

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.
ties.method	Method of breaking ties, passed to base::rank.
simple	Return the p-values only?

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.

See Also

• Basic association test BAT.

• Direct INT test DINT.

• Omnibus INT test OINT.

Examples

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

RNOmni documentation built on Sept. 11, 2023, 9:07 a.m.