RNOmni (version 0.6.0)

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 = 3/8, simple = FALSE, parallel = FALSE)

Arguments

y

Numeric phenotype vector.

G

Obs by snp genotype matrix.

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 only the p-values?

parallel

Logical indicating whether to run in parallel. Must register parallel backend first.

Value

If simple=T, returns a vector of p-values, one for each column of G. If simple=F, 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 DINT, omnibus INT OINT.

Examples

# NOT RUN {
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,simple=T);
# }
# NOT RUN {
;
# }