get_scGateDB: Load scGate model database

In scGate: Marker-Based Cell Type Purification for Single-Cell Sequencing Data

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

scGate load_scGate_model

Examples

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

scGate documentation built on May 29, 2024, 2:56 a.m.