DEAnalyze: Differential expression analysis

In WubingZhang/rMAUPS: Model-Based Analysis of Ubiquitin-Proteome System Based Protein Degradation.

Differential expression analysis

Description

Differential expression analysis

Usage

DEAnalyze(
  obj,
  SampleAnn = NULL,
  type = "Array",
  method = "limma",
  paired = FALSE,
  GeneAnn = NULL,
  return = c("data.frame", "ExpressionSet")[1],
  app.dir = "/Users/Wubing/Applications/gfold/gfold"
)

Arguments

obj	Matrix like object or an ExpressionSet instance.
SampleAnn	Matrix like object (only when obj is a matrix), the rownames should match colnames in obj, and the first column should be Condition.
type	"Array", "RNASeq" or "msms", only needed when obj is matrix like object.
method	Differential expression analysis method, e.g. limma, DESeq2, GFOLD, glm.pois, glm.qlll, and glm.nb.
paired	Boolean, specifying whether perform paired comparison.
GeneAnn	Matrix like object (only when obj is a matrix), the rownames should match rownames of obj.
return	Character, either data.frame or ExpressionSet, specifying the return object type.
app.dir	The path to application (e.g. GFOLD).

Value

An ExpressionSet instance.

Author(s)

Wubing Zhang

See Also

ExpressionSet-class

WubingZhang/rMAUPS documentation built on March 21, 2022, 8:48 p.m.