estimateDispersions: Estimate the dispersions for a DEXSeqDataSet

In areyesq89/DEXSeq: Inference of differential exon usage in RNA-Seq

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", "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.

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 )

areyesq89/DEXSeq documentation built on Oct. 15, 2023, 1:40 p.m.