createGeneSetCommands: Create gene set commands

In iSEEu: iSEE Universe

Description

Create the commands required to populate FeatureSetTables with commonly used gene sets.

Usage

createGeneSetCommands(
  collections = c("GO", "KEGG"),
  organism = "org.Hs.eg.db",
  identifier = "ENTREZID"
)

Arguments

collections	Character vectors specifying the gene set collections of interest.
organism	String containing the org.*.eg.db package to use to extract mappings of gene sets to gene IDs.
identifier	String specifying the identifier to use to extract IDs for the organism package.

Details

GO terms are extracted using the "GOALL" mode, which extracts both direct and indirect children of each term. A description for each GO term is extracted using the GO.db package.

Mappings of genes to KEGG pathway are extracted from the organism package using the "PATH" term. Unfortunately, this is not up to date due to the licensing around KEGG terms. Descriptions for each pathway are extracted from http://rest.kegg.jp/list/pathway.

Value

A list of character vectors describing how to create collections and retrieve gene sets. These can be used as arguments for the FeatureSetTable constructor.

Author(s)

Aaron Lun

See Also

FeatureSetTable, where the commands are intended for use.

setFeatureSetCommands, to use the commands globally.

Examples

out <- createGeneSetCommands()
cat(out$CreateCollections['GO'], "\n")
cat(out$RetrieveSet['GO'], "\n")

iSEEu documentation built on Nov. 8, 2020, 8:12 p.m.