GBJ (version 0.5.4)

OMNI_individual: omni_individual.R

Description

Computes the omnibus test statistic combining GBJ, GHC, minP, and SKAT. This version of the function assumes you have the individual factor data (i.e. genotypes) for each subject. If you only have summary statistics, use omni_ss(). You WILL NOT be able to use this function unless you have also loaded the SKAT package (install.packages("SKAT"); library(SKAT)).

Usage

OMNI_individual(null_model, factor_matrix, link_function, num_boots = 100)

Value

A list with the elements:

OMNI

The observed omnibus test statistic.

OMNI_pvalue

The p-value of the OMNI test

err_code

Sometimes if your p-value is very small (< 1*10^(-10)), R may run into numerical issues. This message will alert you if such a situation occurs.

Arguments

null_model

An R regression model fitted using glm(). Do not use lm(), even for linear regression!

factor_matrix

An n*d matrix with each factor (i.e. each SNP) as one column. There should be no missing data.

link_function

Either "linear" or "logit" or "log".

num_boots

Number of bootstrap repetitions to find correlation matrix of set-based statistics.

Examples

factor_matrix <- matrix(data=rbinom(n=1000, size=2, prob=0.3), ncol=5)
Y <- rnorm(n=200)
null_mod <- glm(Y ~ 1)
OMNI_individual(null_model=null_mod, factor_matrix=factor_matrix,
link_function='linear', num_boots=5)