LRT {lncDIFF}

Likelihood ratio test based on ZIQML.fit()

Description

ZIQML.LRT returns the likelihood ratio test statistics and p-value based on the object returned by ZIQML.fit().

Usage

LRT(ZIQML.fit, coef = NULL)

Arguments

ZIQML.fit

Object returned by ZIQML.fit()

coef

An integer or vector indicating the coefficient(s) in design matrix to be tested. coef=1 is the intercept (i.e. baseline group effect), and should not be tested.

Value

LRT.stat

Likelihood ratio test statistics.

LRT.pvalue

Likelihood ratio test p-value.

Examples

data('hnsc.edata','design')  
# 'hnsc.edata' contains FPKM of 1132 lncRNA genes and 80 samples. 
# 'design' is the design matrix of tissue type (tumor vs normal). 

# Fit GLM by ZIQML.fit for the first 100 genes 
fit.log=ZIQML.fit(edata=hnsc.edata[1:100,],design.matrix=design) 


# Likelihood ratio test to compare tumor vs normal in gene expression level. 
LRT.results=LRT(fit.log,coef=2)