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

SKAT_NULL_emmaX {SKAT} | R Documentation

## 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

[Package SKAT version 2.2.4 Index]