getPantherCollection: Get pathways/GOslim collections from PANTHER.db Biocondcutor...

In lianos/sparrow: Take command of set enrichment analyses through a unified interface

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")

lianos/sparrow documentation built on Feb. 5, 2024, 2:58 p.m.