RNOmni (version 0.1.4)

PIINT: Partially 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 adjustments for population structure.

Usage

PIINT(y, G, X, S, M = T, c = 3/8)

Arguments

y

Numeric phenotype vector.

G

Snp by obs genotype matrix.

X

Obs by feature covariate matrix.

S

Obs by feature structure matrix.

M

Apply missingness filter? See missFilter.

c

Offset applied during rank-normalization. See rankNormal.

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 {
# PIINT against normal phenotype
p = RNOmni::PIINT(y=RNOmni::Y[,1],G=RNOmni::G[1:10,],X=RNOmni::X,S=RNOmni::S);
# }