run.edgeR: Wrapper to run edgeR

View source: R/run.edgeR.r

run.edgeRR Documentation

Wrapper to run edgeR

Description

Wrapper to run edgeR: create the dge object, normalize data, estimate dispersions, statistical testing...

Usage

run.edgeR(
  counts,
  target,
  varInt,
  condRef,
  batch = NULL,
  cpmCutoff = 1,
  normalizationMethod = "TMM",
  pAdjustMethod = "BH",
  ...
)

Arguments

counts

matrix of counts

target

target data.frame of the project

varInt

name of the factor of interest (biological condition)

condRef

reference biological condition

batch

batch effect to take into account (NULL by default)

cpmCutoff

counts-per-million cut-off to filter low counts

normalizationMethod

normalization method: "TMM" (default), "RLE" (DESeq) or "upperquartile"

pAdjustMethod

p-value adjustment method: "BH" (default) or "BY"

...

optional arguments to be passed to glmFit()

Value

A list containing the dge object and the results object

Author(s)

Hugo Varet


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