estimateDispersions {DEXSeq} | R Documentation

## Estimate the dispersions for a DEXSeqDataSet

### Description

This function obtains dispersion estimates for negative binomial distributed data for the specific case for DEXSeq.

### Usage

    ## S4 method for signature 'DEXSeqDataSet'
    estimateDispersions( object, fitType=c("parametric","local","mean"), maxit=100, niter=10, quiet=FALSE, formula=design(object), BPPARAM=SerialParam())

### Arguments

`object` | A DEXSeqDataSet
`fitType` | Either "parametric", "local", or "mean" for the type of fitting of dispersions to the mean intensity. See ?estimateDispersions,DESeqDataSet-method for details.
`maxit` | Control parameter: maximum number of iterations to allow for convergence
`niter` | Number of times to iterate between estimation of means and estimation of dispersion.
`quiet` | Whether to print messages at each step
`formula` | Formula used to fit the dispersion estimates
`BPPARAM` | A "BiocParallelParam" instance. See `?bplapply` for details.

### Details

See ?estimateDispersions,DESeqDataSet-method for details.

### Value

A DEXSeqDataSet with the dispersion information filled in as metadata columns.

### Examples

      data(pasillaDEXSeqDataSet, package="pasilla")
      dxd <- estimateSizeFactors( dxd )
      dxd <- estimateDispersions( dxd )

[Package DEXSeq version 1.38.0 Index]