get_scGateDB {scGate} | R Documentation |
Load scGate model database
Description
Download, update or load local version of the scGate model database. These are stored in a GitHub repository, from where you can download specific versions of the database.
Usage
get_scGateDB(
destination = tempdir(),
force_update = FALSE,
version = "latest",
branch = c("master", "dev"),
verbose = FALSE,
repo_url = "https://github.com/carmonalab/scGate_models"
)
Arguments
destination |
Destination path for storing the DB. The default is tempdir(); if you wish to edit locally the models and link them to the current project, set this parameter to a new directory name, e.g. scGateDB |
force_update |
Whether to update an existing database. |
version |
Specify the version of the scGate_models database (e.g. 'v0.1'). By default downloads the latest available version. |
branch |
branch of the scGate model repository, either 'master' (default) or 'dev' for the latest models |
verbose |
display progress messages |
repo_url |
URL path to scGate model repository database |
Details
Models for scGate are dataframes where each line is a signature for a given filtering level. A database of models can be downloaded using the function
get_scGateDB
. You may directly use the models from the database, or edit one of these models to generate your own custom gating model.
Value
A list of models, organized according to the folder structure of the database. See the examples below.
See Also
Examples
scGate.model.db <- get_scGateDB()
# To see a specific model, browse the list of models:
scGate.model.db$human$generic$Myeloid