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Prepare cell-cell communication databases

Source: R/PrepareCCCDB.R
PrepareCCCDB.Rd

Prepares the ligand-receptor interaction databases used by the cell-cell communication wrappers: the CellTalkDB ligand-receptor pairs ("CellTalk") and the CellChat curated ligand-receptor database ("CellChat"). Each database is returned as a TERM2GENE/TERM2NAME mapping (with a "ligand_*"/"receptor_*" term convention) and cached with R.cache so that ListDB can list it like any other annotation database.

Usage

PrepareCCCDB(
  species = c("Homo_sapiens", "Mus_musculus", "Danio_rerio"),
  db = c("CellChat", "CellTalk"),
  convert_species = TRUE,
  data_dir = NULL,
  db_version = "latest",
  db_update = FALSE,
  verbose = TRUE,
  ...
)

Arguments

species

"Homo_sapiens" or "Mus_musculus".

db

Cell-cell communication databases to prepare. Can be "CellTalk" and/or "CellChat".

convert_species

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

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").

db_version

Database version to retrieve.

db_update

Whether the databases should be forcefully updated. If FALSE, cached databases are reused when available.

verbose

Whether to print the message. Default is TRUE.

...

Passed to helper functions.

Value

A list with the same structure as PrepareDB: for each species a named list of databases, each with TERM2GENE, TERM2NAME, and version entries.

See also

PrepareDB, ListCCCDB, ListDB

Examples

if (FALSE) { # \dontrun{
ccc_db <- PrepareCCCDB(
  species = "Homo_sapiens",
  db = "CellChat"
)
head(ccc_db[["Homo_sapiens"]][["CellChat"]][["TERM2GENE"]])
} # }