RNOmni (version 0.4.0)

IINT: Indirect-INT

Description

Two-stage regression procedure. In the first stage, phenotype is regressed on covariates and structure adjustments to obtain residuals. Genotype is also regressed on covariates and structure adjustments to obtain residuals. In the second stage, INT-transformed phenotypic residuals are regressed on genotypic residuals.

Usage

IINT(y, G, X, S, k = 3/8, parallel = F, check = T)

Arguments

y

Numeric phenotype vector.

G

Obs by snp genotype matrix.

X

Model matrix of covariates.

S

Model matrix of structure adjustments.

k

Offset applied during rank-normalization. See rankNormal.

parallel

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

check

Logical indicating whether to check the input.

Value

A numeric matrix of Wald statistics and p-values, one for each locus (column) in G, assessing the null hypothesis that genotype is unrelated to the phenotype.

Examples

# NOT RUN {
# IINT against normal phenotype 
p = RNOmni::IINT(y=RNOmni::Y[,1],G=RNOmni::G[,1:10],X=RNOmni::X,S=RNOmni::S);
# }