dispersionFunction: Accessors for the 'dispersionFunction' slot of a DESeqDataSet...

In nlhuong/ZeroInflatedDESeq2: Differential gene expression analysis based on the negative binomial distribution

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)

nlhuong/ZeroInflatedDESeq2 documentation built on May 23, 2019, 9:06 p.m.