NgsProjectClass: R6 class for project information

In hcnh174/hlsgr: Hiroshima Liver Study Group R Utilities

R6 class for project information

Description

R6 class for project information

R6 class for project information

Super class

hlsgr::AbstractBaseClass -> NgsProjectClass

Methods

Public methods

• NgsProjectClass$new()

• NgsProjectClass$getGroupLevels()

• NgsProjectClass$getSamplesByGroup()

• NgsProjectClass$getCountsByGroup()

• NgsProjectClass$getDatTraits()

• NgsProjectClass$createDeseq2ClassFromCounts()

• NgsProjectClass$createDeseq2ClassFromSalmon()

• NgsProjectClass$createEdgeRClassFromCounts()

• NgsProjectClass$createEdgeRClassFromSalmon()

• NgsProjectClass$createLimmaVoomClassFromCounts()

• NgsProjectClass$createLimmaVoomClassFromSalmon()

• NgsProjectClass$clone()

Inherited methods

---

Method new()

Usage

NgsProjectClass$new(dir)

Arguments

dir

folder containing project and sample information

---

Method getGroupLevels()

Usage

NgsProjectClass$getGroupLevels(groupcol)

Arguments

groupcol

group column

Returns

Examples

getGroupLevels(project, groupcol='default')
getSamplesByGroup

---

Method getSamplesByGroup()

Usage

NgsProjectClass$getSamplesByGroup(groupcol)

Arguments

groupcol

group column

Returns

---

Method getCountsByGroup()

Usage

NgsProjectClass$getCountsByGroup(counts, groupcol)

---

Method getDatTraits()

Usage

NgsProjectClass$getDatTraits(cols)

---

Method createDeseq2ClassFromCounts()

Usage

NgsProjectClass$createDeseq2ClassFromCounts(
  rnaseq,
  groupcol,
  outdir,
  identifier = "ensembl_id"
)

---

Method createDeseq2ClassFromSalmon()

Usage

NgsProjectClass$createDeseq2ClassFromSalmon(salmon, groupcol, outdir)

---

Method createEdgeRClassFromCounts()

Usage

NgsProjectClass$createEdgeRClassFromCounts(
  rnaseq,
  groupcol,
  outdir,
  identifier = "ensembl_id"
)

---

Method createEdgeRClassFromSalmon()

Usage

NgsProjectClass$createEdgeRClassFromSalmon(salmon, groupcol, outdir)

---

Method createLimmaVoomClassFromCounts()

Usage

NgsProjectClass$createLimmaVoomClassFromCounts(
  rnaseq,
  groupcol,
  outdir,
  identifier = "ensembl_id"
)

---

Method createLimmaVoomClassFromSalmon()

Usage

NgsProjectClass$createLimmaVoomClassFromSalmon(salmon, groupcol, outdir)

---

Method clone()

The objects of this class are cloneable with this method.

Usage

NgsProjectClass$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

project <- NgsProjectClass$new(projectdir)
getGroupLevels returns unique ordered levels for specified group


## ------------------------------------------------
## Method `NgsProjectClass$getGroupLevels`
## ------------------------------------------------

getGroupLevels(project, groupcol='default')
getSamplesByGroup

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