getKeggCollection {sparrow} | R Documentation

## Retrieves the KEGG gene set collection via its REST API

### Description

Uses `limma::getGeneKEGGLinks()` and `limma::getKEGGPathwayNames()` internally.

### Usage

    getKeggCollection(species = "human", id.type = c("ensembl", "entrez"), ...)

    getKeggGeneSetDb(species = "human", id.type = c("ensembl", "entrez"), ...)

### Arguments

`species` | `"human"`, `"mouse"` or any of the bioconductor or kegg-style abbreviations.
`id.type` | Gene identifiers are returned by the REST service as entrez identifiers. Set this to `"ensembl"` to translate them internally using `convertIdentifiers()`. If `species`is not `"human"` or `"mouse"`, you need to provide an idxref table that works with `convertIdentifiers()`.
`...` | pass through arguments

### Details

Currently we just support the pathway database, and only entrez ids.

Note that it is your responsibility to ensure that you can use the KEGG database according to their licensing requirements.

### Value

A BiocSet of the kegg stuffs

### Functions

- `getKeggGeneSetDb`: method that returns a GeneSetDb

### Examples

    # connects to the internet and takes a while
    mouse.entrez <- getKeggCollection("mouse", id.type = "entrez")
    human.enrez <- getKeggCollection("human", id.type = "entrez")

[Package sparrow version 1.0.3 Index]