non-standardized globaltest {ctgt} R Documentation

## 'Non-standardized globaltest'

### Description

This is the sencond version of the globaltest, the non-standardized globaltest

### Usage

  ## a powerful variant of globaltest
gt2 (y, X, hyps, alpha = 0.05)



### Arguments

 y The response vector (numeric vector). X The full design matrix, whose columns are named by the covariates. hyps The name vector of the covariates in the pathway of interest (character vector). alpha The type I error rate allowed. The default is 0.05.

### Value

Returns the p-value, the observed and expected test statistics and the number of covariates.

### Author(s)

Ningning Xu

Maintainer: Ningning Xu <n.xu@lumc.nl; xu15263142750@gmail.com>

### References

Ningning Xu, Aldo solari, Jelle Goeman, Clsoed testing with global test, with applications on metabolomics data, arXiv:2001.01541, https://arxiv.org/abs/2001.01541

### Examples

  #Generate the design matrix and response vector for logistic regression models
n= 100
m = 5
X = matrix(data = 0, nrow = n, ncol = m,byrow = TRUE )
for ( i in 1:n){
set.seed(1234+i)
X[i,] =  as.vector(arima.sim(model = list(order = c(1, 0, 0), ar = 0.2), n = m) )
}

y = rbinom(n,1,0.6)
X[which(y==1),1:3] = X[which(y==1),1:3] + 0.8

xs = paste("x",seq(1,m,1),sep="")
colnames(X) = xs

hyps=xs[1]

#The raw p-values of globaltest
gt2(y = y, X = X, hyps = hyps, alpha = 0.05)
#p-value Statistic  Expected      #Cov
#7.64e-03  2.30e+02  1.24e+02  1.00e+00


[Package ctgt version 2.0.1 Index]