createGeneSetCommands {iSEEu} | R Documentation

## 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")

[Package iSEEu version 1.4.0 Index]