RNOmni (version 0.6.0)

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, test = "Score", simple = FALSE,
  parallel = FALSE)

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.

test

Either Score or Wald.

simple

Return only the p-values?

parallel

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

Value

If simple=T, returns a vector of p-values, one for each column of G. If simple=F, returns a numeric matrix, including the Wald or Score statistic, its standard error, the Z-score, and the p-value.

See Also

Direct INT DINT, indirect INT IINT, omnibus INT OINT.

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,simple=T);
# }