getPantherCollection {sparrow} | R Documentation

## Get pathways/GOslim collections from PANTHER.db Biocondcutor package.

### Description

This is a convience function that orchestrates the PANTHER.db package to return GeneSetDb objects for either pathway or GOslim information for human or mouse.

### Usage

    getPantherCollection(
      type = c("pathway", "goslim"),
      species = c("human", "mouse")
    )

    getPantherGeneSetDb(
      type = c("pathway", "goslim"),
      species = c("human", "mouse")
    )

### Arguments

`type` | "pathway" or, "goslim"
`species` | "human" or "mouse"

### Details

Note that for some reason the `PANTHER.db` package needs to be installed in a user-writable package location for this to work properly. If you see an error like "Error in resqlite_send_query ... attempt to write a readonly database", this is the problem. Please install another version of the `PANTHER.db` package in a user-writable directory using `BiocManager::install()`.

### Value

A BiocSet of panther pathways

### Functions

- `getPantherGeneSetDb`: returns a GeneSetDb

### GOSLIM

GO Slims are "cut down" versions of the GO ontology that contain a subset of the terms in the whole GO.

PANTHER provides their own set of GO slims, although it's not clear how often these get updated.

### Examples

    # this requires you have the PANTHER.db package installed via BiocManager
    bsc.panther <- getPantherCollection(species = "human")

[Package sparrow version 1.0.3 Index]