DEXSeq (version 1.18.4)

estimateDispersions: Estimate the dispersions for a DEXSeqDataSet

Description

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

Usage

"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.

Value

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

Details

See ?estimateDispersions,DESeqDataSet-method for details.

Examples

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