getPantherGeneSetDb: Get pathways/GOslim information from PANTHER.db Biocondcutor...

In lianos/multiGSEA: A unified interface to a plethora of gene set enrichment analysis methods

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.

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().

Usage

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

getGOslimGeneSetDb(species = c("human", "mouse"))

Arguments

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

Value

A wired up 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.

lianos/multiGSEA documentation built on Nov. 17, 2020, 1:26 p.m.