createGeneSetCommands: Create gene set commands

In csoneson/iSEEu: iSEE Universe

Create gene set commands

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.

The output of this function can be used as the commands argument of registerFeatureSetCommands. It is also used by default in the FeatureSetTable constructor when no collections are registered.

Value

A list of two character vectors describing how to create collections and retrieve gene sets. This follows the expectations for commands in registerFeatureSetCommands.

Author(s)

Aaron Lun

See Also

FeatureSetTable, where the commands are intended for use.

registerFeatureSetCommands, to use the commands globally.

Examples

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

csoneson/iSEEu documentation built on Oct. 16, 2024, 4:50 a.m.