ZIQML.fit {lncDIFF}

Group and covariate effects on lncRNA counts by Generalized Linear Model

Description

ZIQML.fit estimates the group effect on gene expression 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 and covariates, 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 gene expression by zero-inflated exponential quasi maximum likelihood (ZIQML) estimator.

logLikelihood

The value of zero-inflated quasi likelihood.

edata

lncRNA counts or expression matrix.

design.matrix

The design matrix of groups and covariates.

link

The specified link function.

Examples

data('hnsc.edata','design') 
# 'hnsc.edata' contains FPKM of 1000 lncRNA genes and 80 samples 
# 'design' is the design matrix for tissue and batch.

# For the first 100 genes  
# Fit GLM by ZIQML with logarithmic link function                                      
fit.log=ZIQML.fit(edata=hnsc.edata[1:100,],design.matrix=design,link='log') 

# Fit GLM by ZIQML with identity link function
fit.identity=ZIQML.fit(edata=hnsc.edata[1:100,],design.matrix=design,link='identity')