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

In mikelove/DESeq2: Differential gene expression analysis based on the negative binomial distribution

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) <- value

Arguments

object	a DESeqDataSet object.
...	additional arguments
value	a function

Details

Using this setter function will also overwrite mcols(object)$dispFit and the estimate of the variance of dispersion residuals.

See Also

estimateDispersions

Examples

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

mikelove/DESeq2 documentation built on July 25, 2024, 11:11 p.m.