DESeq (version 1.24.0)

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
## S3 method for class 'DESeqDataSet':
dispersionFunction(object)
## S3 method for class '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)