LRT: Likelihood ratio test based on ZIQML.fit()

In lncDIFF: Long Non-Coding RNA Differential Expression Analysis

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)  

lncDIFF documentation built on Jan. 17, 2020, 9:06 a.m.