IINT {RNOmni} | R Documentation |
Two-stage 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 INT-transformed
residuals are regressed on the genotypic residuals.
IINT(y, G, X = NULL, k = 3/8, simple = FALSE, parallel = FALSE)
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
|
simple |
Return the p-values only? |
parallel |
Logical indicating whether to run in parallel. Must register parallel backend first. |
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.
Basic association test BAT
, direct INT DINT
, omnibus INT OINT
.
## 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 = IINT(y=y,G=G,X=X,simple=T); ## End(Not run);