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

In aghozlane/DESeq2shaman: 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)<-value

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

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.

Examples

example("estimateDispersions")
dispersionFunction(dds)

aghozlane/DESeq2shaman documentation built on Nov. 1, 2019, 9:01 p.m.