SKAT_NULL_emmaX: Get parameters and residuals from the null model with...

In SKAT: SNP-Set (Sequence) Kernel Association Test

Get parameters and residuals from the null model with incorporating the kinship structure

Description

Compute model parameters and residuals for SKAT with incorporating the kinship structure.

Usage

SKAT_NULL_emmaX (formula, data=NULL, K=NULL, 
Kin.File=NULL, ngrids=100, llim=-10, ulim=10, esp=1e-10, Is.GetEigenResult=FALSE) 
  
 

Arguments

formula	an object of class “formula”: a symbolic description of the NULL model to be fitted.
data	an optional data frame containing the variables in the model (default=NULL). If it is NULL, the variables are taken from 'environment(formula)'
K	a kinship matrix. If K=NULL, the function reads Kin.File to get a kinship matrix.
Kin.File	an emmax-kin output file name. If K=NULL, the function reads this file.
ngrids	Number of grids to search for the optimal variance component
llim	Lower bound of log ratio of two variance components
ulim	Upper bound of log ratio of two variance components
esp	Tolerance of numerical precision error
Is.GetEigenResult	Return intermediate eigen-decomposition results

Details

The Emma package code was used to implement this function.

Resampling is not implemented.

Value

This function returns an object that has model parameters and residuals of the NULL model of no associations. After obtaining it, use SKAT function to carry out the association test.

Author(s)

Seunggeun Lee

Examples

data(SKAT.fam.example)

K = SKAT.fam.example$K
Z = SKAT.fam.example$Z
obj<-SKAT_NULL_emmaX(y ~ X, K=K, data=SKAT.fam.example)
SKAT(Z, obj)$p.value

# SKAT-O
SKAT(Z, obj, method="optimal.adj")$p.value	

SKAT documentation built on Jan. 15, 2023, 5:10 p.m.