RNOmni (version 0.5.0)

DINT: Direct-INT

Description

Applies the rank-based inverse normal transformation (rankNorm) to the phenotype y. Conducts tests of association between the loci in G and transformed phenotype, adjusting for the model matrix X.

Usage

DINT(y, G, X = NULL, k = 3/8, parallel = F)

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.

parallel

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

Value

A numeric matrix of score statistics and p-values, one for each locus (column) in G, assessing the null hypothesis of no genetic effect.

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 = DINT(y=y,G=G,X=X);
# }