callDEs {ABSSeq} | R Documentation

## 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", 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

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

[Package ABSSeq version 1.44.0 Index]