ZIQML.fit: Group effect estimate on lncRNA normalized counts

In qianli10000/lncDIFF: lncRNA Normalized Counts Differential Expression Analysis

Description

ZIQML.fit estimates the group effect on genes using zero-inflated exponential quasi likelihood.

Usage

ZIQML.fit(edata, design.matrix, link = "log")

Arguments

edata	Normalized counts matrix with genes in rows and samples in columns.
design.matrix	Design matrix for groups, generated by model.matrix().
link	Link function for the generalized linear model and likelihood function,either 'log' or 'identity'. The default is 'log'.

Value

Estimates	Estimated group effect on input genes by zero-inflated exponential quasi maximum likelihood (ZIQML) estimator.
logLikelihood	The value of zero-inflated quasi likelihood at estimated group effect.
edata	The input gene expression matrix.
design.matrix	The input design matrix.
link	The specified link function.

Examples

data('tcga.hnsc.match.edata','design') 
# 'tcga.hnsc.match.edata' contains RPKM of 1132 lncRNA genes and 80 samples 
# 'design' is the design matrix for tumor vs normal tissue.
                                       
fit.log=ZIQML.fit(edata=tcga.hnsc.match.edata,design.matrix=design,link='log') 
# Fit GLM by ZIQML with logarithmic link function 

fit.identity=ZIQML.fit(edata=tcga.hnsc.match.edata,design.matrix=design,link='identity') 
# Fit GLM by ZIQML with identity link function

qianli10000/lncDIFF documentation built on Feb. 2, 2020, 6:46 p.m.