RNOmni (version 0.2.1)

BAT: Basic Association Test

Description

Tests the association between genotype and the untransformed phenotype, adjusting for covariates and population structure.

Usage

BAT(y, G, X, S, calcP = T, parallel = F)

Arguments

y

Numeric phenotype vector.

G

Numeric snp by obs genotype matrix.

X

Numeric obs by feature covariate matrix.

S

Numeric obs by feature structure matrix.

calcP

Logical indicating that p values should be calculated.

parallel

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

Value

A numeric matrix of score statistics, one for each locus (row) in G, assessing the null hypothesis that genotype is unrelated to the outcome. If p=T, a p-value is additionally calculated for each locus.

Examples

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