RNOmni (version 0.5.0)

BAT: Basic Association Test

Description

Conducts tests of association between the loci in G and the untransformed phenotype y, adjusting for the model matrix X.

Usage

BAT(y, G, X = NULL, 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.

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 = as.numeric(X%*%c(1,1))+rnorm(1e3);
# Association test
p = BAT(y=y,G=G,X=X);
# }