gsets: A genesets object

In montilab/hypeR: An R Package For Geneset Enrichment Workflows

A genesets object

Description

A genesets object

A genesets object

See Also

rgsets

Public fields

genesets

A named list of genesets

name

A character vector describing source of genesets

version

A character vector describing versioning

Methods

Public methods

• gsets$new()

• gsets$print()

• gsets$list()

• gsets$info()

• gsets$reduce()

• gsets$clone()

---

Method new()

Create a gsets object

Usage

gsets$new(
  genesets,
  name = "Custom",
  version = "",
  clean = FALSE,
  quiet = FALSE
)

Arguments

genesets

A named list of genesets

name

A character vector describing source of genesets

version

A character vector describing versioning

clean

Use true to clean labels of genesets

quiet

Use true to silence warnings

Returns

A new gsets object

---

Method print()

Print genesets information

Usage

gsets$print()

Returns

NULL

---

Method list()

Return genesets as a list

Usage

gsets$list()

Returns

A list of genesets

---

Method info()

Returns versioning information

Usage

gsets$info()

Returns

A character vector with name and version

---

Method reduce()

Reduces genesets to a background distribution of symbols

Usage

gsets$reduce(background)

Arguments

background

A character vector of symbols

Returns

A gsets object

---

Method clone()

The objects of this class are cloneable with this method.

Usage

gsets$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

genesets <- list("GSET1" = c("GENE1", "GENE2", "GENE3"),
                 "GSET2" = c("GENE4", "GENE5", "GENE6"),
                 "GSET3" = c("GENE7", "GENE8", "GENE9"))

gsets_obj <- gsets$new(genesets, name="example", version="v1.0")
print(gsets_obj)

montilab/hypeR documentation built on Oct. 29, 2023, 12:01 p.m.