Estimate the dispersions for a DEXSeqDataSet — estimateDispersions • DEXSeq

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

Usage

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

Arguments

object: A DEXSeqDataSet.
fitType: Either "parametric", "local", "mean" or "glmGamPoi" for the type of fitting of dispersions to the mean intensity. See ?estimateDispersions,DESeqDataSet-method for details. If "glmGamPoi" is selected, the GLM fitter from "glmGamPoi" is also used for estimating the dispersion estimates.
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 )