callParameter {ABSSeq} | R Documentation

## Calculate parameters for differential expression test base on absolute counts differences

### Description

Calculate parameters for each gene (the moderating basemean, dispersions, moderated fold-change and general sd)

### Usage

    callParameter(object, replaceOutliers = TRUE, ...)

### Arguments

`object` | a `ABSDataSet` object.
`replaceOutliers` | switch for outlier replacement, default is TRUE.
`...` | parameters past to `ReplaceOutliersByMAD`

### Details

shifted and calculate a set of parameters from normalized counts table before `callDEs`

### Value

A ABSDataSet object with absolute differences, basemean, mean of each group, variance, log2 of foldchange, named as 'absD', 'baseMean', 'Amean', 'Bmean', 'Variance' and 'foldChange', respectively. Use the `results` to get access it and `plotDifftoBase` to plot it.

### Note

This function should run after `normalFactors` or providing size factors.

### Examples

    data(simuN5)
    obj <- ABSDataSet(counts=simuN5$counts, groups=factor(simuN5$groups))
    obj <- normalFactors(obj)
    obj <- callParameter(obj)
    head(results(obj,c("foldChange","absD","baseMean")))
    plotDifftoBase(obj)

[Package ABSSeq version 1.44.0 Index]