callDEs: Testing the differential expression by counts difference

Description Usage Arguments Details Value Note Examples

View source: R/functions.R

Description

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

Usage

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callDEs(object, adjmethod = "BH", useaFold = FALSE)

Arguments

object

an ABSDataSet object.

adjmethod

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

useaFold

switch for DE detection through fold-change, which will use a normal distribution (N(0,sd)) to test the significance of log2 fold-change. The sd is estimated through a quantile function of gamma distribution at callParameter.

Details

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

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.

Note

this function should run after callParameter

Examples

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ABSSeq documentation built on July 26, 2017, 2 a.m.

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