IINT  R Documentation 
Twostage association testing procedure. In the first stage, phenotype
y
and genotype G
are each regressed on the model matrix
X
to obtain residuals. The phenotypic residuals are transformed
using RankNorm
. In the next stage, the INTtransformed
residuals are regressed on the genotypic residuals.
IINT(y, G, X = NULL, k = 0.375, ties.method = "average", simple = FALSE)
y 
Numeric phenotype vector. 
G 
Genotype matrix with observations as rows, SNPs as columns. 
X 
Model matrix of covariates and structure adjustments. Should include an intercept. Omit to perform marginal tests of association. 
k 
Offset applied during ranknormalization. See

ties.method 
Method of breaking ties, passed to 
simple 
Return the pvalues only? 
If simple = TRUE
, returns a vector of pvalues, one for each column
of G
. If simple = FALSE
, returns a numeric matrix, including the
Wald or Score statistic, its standard error, the Zscore, and the pvalue.
Basic association test BAT
.
Direct INT test DINT
.
Omnibus INT test OINT
.
set.seed(100)
# Design matrix
X < cbind(1, stats::rnorm(1e3))
# Genotypes
G < replicate(1e3, stats::rbinom(n = 1e3, size = 2, prob = 0.25))
storage.mode(G) < "numeric"
# Phenotype
y < exp(as.numeric(X %*% c(1,1)) + stats::rnorm(1e3))
# Association test
p < IINT(y = y, G = G, X = X)
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