get_scGateDB: 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"
)

Value

A list of models, organized according to the folder structure of the database. See the examples below.

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.

Examples

Run this code

scGate.model.db <- get_scGateDB()
# To see a specific model, browse the list of models:
scGate.model.db$human$generic$Myeloid