ABSSeq (version 1.8.0)

callDEs: Testing the differential expression by counts difference

Description

Using NB distribution to calculate p-value for each gene as well as adjust p-value

Usage

callDEs(object, adjmethod = "BH")

Arguments

object

an ABSDataSet object.

adjmethod

the method for adjusting p-value, default is 'BH'. For details, see p.adjust.methods.

Value

an ABSDataSet object with additional elements: shrinked log2 fold-change, pvalue and adjusted p-value, denoted by foldChange pvalue and adj-pvalue, respectively. Use the results method to get access it.

Details

This function firstly calls p-value used pnbinom to call pvalue based on sum of counts difference between two groups, then adjusts the pvalues via p.adjust method. In addition, it also shrink the log2 fold-change towards a common dispersion after pvalue calling.

Examples

data(simuN5)
obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups))
obj <- normalFactors(obj)
obj <- callParameter(obj)
obj <- callDEs(obj)
head(results(obj))