msigdb_retrieve: Retrieves a msgidb collection data.frame for the given...

In lianos/GeneSetDb.MSigDB: Data package for query/retrieval of species specific MSigDB versions

Description

This function retrieves arbitrary subset of the MSigDB collections, which are determined by the values passed into collections. This parameter is a character vector that can be any of the collections themselves (ie. "H", C1:C7).

Usage

msigdb_retrieve(
  collections = "H",
  species = "human",
  id_type = c("ensembl", "entrez", "symbol"),
  version = NULL,
  minimal = TRUE,
  allow_multimap = TRUE,
  min_ortho_sources = 2,
  promote_subcategory_to_collection = FALSE,
  go_slim = FALSE,
  cache = TRUE,
  ...
)

Arguments

collections	character of MSigDb collections ("h", "c1", ..., "c7")
species	the name of the species (human, mouse, etc.) see entries in msigdb.data:::.species_tbl()["common_name] (+ "human")
id_type	"ensembl", "entrez", or "symbol"
version	if NULL (default), the latest will be returned.
allow_multimap	If TRUE (default), multiple entries are returned for a single gene in the original dataset, in the event that a single human,entrez identifier maps to more than one ensembl identifier.
min_ortho_sources	Filter the hcop table on num_sources column to ensure a minimum number of databases that support the ortholog map
promote_subcategory_to_collection	When TRUE (default is FALSE), the database collections in C2 (like reactome, biocarta) will be pulled out of the c2 collection and promoted to their own (ie. there will be "reactome_c2" collection).
go_slim	Allows user to cut down the gene ontology collection (C5) to a subset ("slims"). By default, this is set to FALSE, which indicates no slimming. Setting to TRUE will slim down to the "generic" subsets. More subsets, will be added in time, http://geneontology.org/docs/download-ontology/#subsets

Details

The C2 collection includes subets of curated databases in it, such as biocarta, kegg, pid, and reactome. You can also use these identifiers in the collections parameter if you don't want to retrieve all of C2. When the promote_subcategory_to_collection is TRUE, these databases will be pulled out of the C2 collection, and promoted to their own collections, themselves. The C5/GO annotations will also be split up into three collecionts, GO_MF, GO_CC, GO_BP.

Value

a geneset data.frame with the msigdb collecitons mapped to the given species. This result can be passed into multiGSEA::GeneSetDb() to get gene set mojo started.

lianos/GeneSetDb.MSigDB documentation built on June 16, 2020, 1:39 a.m.