run.edgeR_trans: Wrapper to run edgeR

In sarangian/RNASeqDEA: Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups

Description

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

Usage

run.edgeR_trans(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

sarangian/RNASeqDEA documentation built on Dec. 8, 2019, 5:24 p.m.