DeSeq2Class: R6 class for DESeq2 analysis

In hcnh174/hlsgr: Hiroshima Liver Study Group R Utilities

R6 class for DESeq2 analysis

Description

R6 class for DESeq2 analysis

R6 class for DESeq2 analysis

Super classes

hlsgr::AbstractBaseClass -> hlsgr::AbstractDifferentialExpressionAnalysisClass -> DeSeq2Class

Methods

Public methods

• DeSeq2Class$new()

• DeSeq2Class$getResults()

• DeSeq2Class$makeTable()

• DeSeq2Class$createWgcnaClass()

• DeSeq2Class$clone()

Inherited methods

---

Method new()

Usage

DeSeq2Class$new(dds, outdir, identifier = "ensembl_id")

Arguments

outdir

directory to write DGE results to

---

Method getResults()

Usage

DeSeq2Class$getResults(p = NULL, padj = 0.05, logfc = 1.5, n = NULL)

---

Method makeTable()

Usage

DeSeq2Class$makeTable(num = 50, padj = 1, lfc = 1.5)

---

Method createWgcnaClass()

Usage

DeSeq2Class$createWgcnaClass(
  datTraits,
  p = NULL,
  padj = NULL,
  logfc = NULL,
  n = 5000
)

Arguments

datTraits

Examples

wgcna <- deseq2$createWgcnaClass(datTraits)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

DeSeq2Class$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

project <- DeSeq2Class$new(salmon, groupcol, outdir)
createWgcnaClass


## ------------------------------------------------
## Method `DeSeq2Class$createWgcnaClass`
## ------------------------------------------------

wgcna <- deseq2$createWgcnaClass(datTraits)

hcnh174/hlsgr documentation built on April 7, 2023, 4:02 p.m.