DESeq2: dispersionFunction – R documentation

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dispersionFunction

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.

Examples

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

DESeq2

Differential gene expression analysis based on the negative binomial distribution

v1.30.1

LGPL (>= 3)

Authors

Michael Love [aut, cre], Constantin Ahlmann-Eltze [ctb], Kwame Forbes [ctb], Simon Anders [aut, ctb], Wolfgang Huber [aut, ctb]

Initial release