run.DESeq2: Wrapper to run DESeq2

In PF2-pasteur-fr/SARTools: Statistical Analysis of RNA-Seq Tools

Wrapper to run DESeq2

Description

Wrapper to run DESeq2: create the DESeqDataSet, normalize data, estimate dispersions, statistical testing...

Usage

run.DESeq2(
  counts,
  target,
  varInt,
  batch = NULL,
  locfunc = "median",
  fitType = "parametric",
  pAdjustMethod = "BH",
  cooksCutoff = TRUE,
  independentFiltering = TRUE,
  alpha = 0.05,
  ...
)

Arguments

counts	matrix of raw counts
target	target data.frame of the project
varInt	name of the factor of interest (biological condition)
batch	batch effect to take into account (NULL by default)
locfunc	"median" (default) or "shorth" to estimate the size factors
fitType	mean-variance relationship: "parametric" (default) or "local"
pAdjustMethod	p-value adjustment method: "BH" (default) or "BY" for instance
cooksCutoff	outliers detection threshold (TRUE to let DESeq2 choosing it or FALSE to disable the outliers detection)
independentFiltering	TRUE or FALSE to perform the independent filtering or not
alpha	significance threshold to apply to the adjusted p-values
...	optional arguments to be passed to nbinomWaldTest()

Value

A list containing the dds object (DESeqDataSet class), the results objects (DESeqResults class) and the vector of size factors

Author(s)

Hugo Varet

PF2-pasteur-fr/SARTools documentation built on April 6, 2022, 2:24 a.m.