dispersionFunction {DESeq2} | R Documentation

## Accessors for the 'dispersionFunction' slot of a DESeqDataSet object.

### Description

The dispersion function is calculated by `estimateDispersions` and used by `varianceStabilizingTransformation`. Parametric dispersion fits store the coefficients of the fit as attributes in this slot.

### Usage

    dispersionFunction(object, ...)

    dispersionFunction(object, ...) <- value

    ## S4 method for signature 'DESeqDataSet'
    dispersionFunction(object)

    ## S4 replacement method for signature 'DESeqDataSet,'function''
    dispersionFunction(object,
      estimateVar = TRUE) <- value

### Arguments

`object` | a `DESeqDataSet` object.
`...` | additional arguments
`value` | a `function`
`estimateVar` | whether to estimate the variance of dispersion residuals. setting to FALSE is needed, e.g. within `estimateDispersionsMAP` when called on a subset of the full dataset in parallel execution.

### Details

Setting this will also overwrite `mcols(object)$dispFit` and the estimate the variance of dispersion residuals, see `estimateVar` below.

### See Also

`estimateDispersions`

### Examples

    dds <- makeExampleDESeqDataSet(m=4)
    dds <- estimateSizeFactors(dds)
    dds <- estimateDispersions(dds)
    dispersionFunction(dds)

[Package DESeq2 version 1.20.0 Index]