RNOmni (version 0.2.1)

IINT: Indirect-INT

Description

Two-stage regression procedure. In the first stage, phenotype is regressed on covariates to obtain residuals. In the second stage, INT-transformed residuals are regressed on genotype and population structure.

Usage

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

Arguments

y

Numeric phenotype vector.

G

Snp by obs genotype matrix.

X

Obs by feature covariate matrix.

S

Obs by feature structure matrix.

calcP

Logical indicating that p values should be calculated.

k

Offset applied during rank-normalization. See rankNormal.

parallel

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

Value

A numeric vector of p-values assessing the null hypothesis of no genotypic effect. P-values are estimated using the Wald statistic, and correspond to the rows of G.

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);
# }