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Prepare MSigDB databases

Source: R/PrepareDBPathway.R
PrepareMSigDB.Rd

Prepare MSigDB annotations, reusing the common cache and species/identifier conversion pipeline.

Usage

PrepareMSigDB(
  species = c("Homo_sapiens", "Mus_musculus"),
  db = "MSigDB",
  db_IDtypes = c("symbol", "entrez_id", "ensembl_id"),
  db_version = "latest",
  db_update = FALSE,
  data_dir = NULL,
  convert_species = TRUE,
  Ensembl_version = NULL,
  mirror = NULL,
  biomart = NULL,
  max_tries = 5,
  verbose = TRUE,
  ...
)

Arguments

species

"Homo_sapiens" or "Mus_musculus".

db

Character vector selecting "MSigDB" or "MSigDB_<collection>".

db_IDtypes

Gene ID types to include.

db_version

Database version to retrieve.

db_update

Force a refresh. FALSE loads the cache when available.

data_dir

Directory or named list of local source files. Searches data_dir/<db>/ then data_dir. Named lists override a path, e.g. list(MSigDB = "~/db/msigdb").

convert_species

Use a species-converted database when the annotation is missing for species.

Ensembl_version

Ensembl version. NULL uses the latest.

mirror

Specify an Ensembl mirror to connect to. The valid options here are "www", "uswest", "useast", "asia".

biomart

BioMart database that you want to connect to. Possible options include "ensembl", "protists_mart", "fungi_mart", and "plants_mart".

max_tries

The maximum number of attempts to connect with the BioMart service.

verbose

Whether to print the message. Default is TRUE.

...

Passed to helper functions.

Value

A named species list containing the selected databases. Annotation entries contain TERM2GENE, TERM2NAME and version.

Details

Collections can be selected with MSigDB_<collection>, including nested prefixes such as MSigDB_M2_CP_BIOCARTA. Colon forms are accepted.

See also

PrepareDB, ListDB

Examples

if (FALSE) { # \dontrun{
databases <- PrepareMSigDB(species = "Homo_sapiens", db = "MSigDB")
names(databases[["Homo_sapiens"]])
} # }