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Prepare databases and reference resources

Source: R/PrepareDB.R
PrepareDB.Rd

Prepare species-specific databases and reference resources from annotation packages, cached downloads, or supplied files.

Usage

PrepareDB(
  species = c("Homo_sapiens", "Mus_musculus"),
  db = c("GO", "GO_BP", "GO_CC", "GO_MF", "KEGG", "WikiPathway", "Reactome", "CORUM",
    "MP", "DO", "HPO", "PFAM", "CSPA", "Surfaceome", "SPRomeDB", "VerSeDa", "TFLink",
    "hTFtarget", "TRRUST", "JASPAR", "ENCODE", "MSigDB", "CellTalk", "CellChat",
    "Chromosome", "GeneType", "Enzyme", "TF", "CytoTRACE2"),
  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,
  custom_TERM2GENE = NULL,
  custom_TERM2NAME = NULL,
  custom_species = NULL,
  custom_IDtype = NULL,
  custom_version = NULL,
  verbose = TRUE,
  ...
)

Arguments

species

"Homo_sapiens" or "Mus_musculus".

db

Character vector of database or resource selectors: "GO", "GO_BP", "GO_CC", "GO_MF", "KEGG", "WikiPathway", "Reactome", "CORUM", "MP", "DO", "HPO", "PFAM", "Chromosome", "GeneType", "Enzyme", "TF", "CSPA", "Surfaceome", "SPRomeDB", "VerSeDa", "TFLink", "hTFtarget", "TRRUST", "JASPAR", "ENCODE", "MSigDB", "CellTalk", "CellChat", "CytoTRACE2" or "MSigDB_<collection>". A vector may combine sources. See the corresponding preparation function for source-specific settings.

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.

custom_TERM2GENE, custom_TERM2NAME

Custom mappings for custom_species.

custom_species, custom_IDtype, custom_version

Metadata for a custom database.

verbose

Whether to print the message. Default is TRUE.

...

Passed to helper functions.

Value

A named list of prepared resources. Gene annotation databases are nested by species and database, with TERM2GENE (gene-to-term mappings), TERM2NAME (term names) and version. Additional resource fields follow the return contract of the corresponding preparation function.

See also

ListDB, PrepareGO, PrepareKEGG, PrepareMSigDB, PrepareIREA

Examples

if (FALSE) { # \dontrun{
databases <- PrepareDB(species = "Homo_sapiens", db = c("GO_BP", "KEGG"))
names(databases[["Homo_sapiens"]])
ListDB(species = "Homo_sapiens", db = c("GO_BP", "KEGG"))
} # }