load_scGate_model: Load a single scGate model

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

Load a single scGate model

Description

Loads a custom scGate model into R. For the format of these models, have a look or edit one of the default models obtained with get_scGateDB

Usage

load_scGate_model(model_file, master.table = "master_table.tsv")

Arguments

model_file	scGate model file, in .tsv format.
master.table	File name of the master table (in repo_path folder) that contains cell type signatures.

Value

A scGate model in dataframe format, which can given as input to the scGate function.

See Also

scGate get_scGateDB

Examples

dir <- tempdir() # this may also be set to your working directory
models <- get_scGateDB(destination=dir)
# Original or edited model
model.path <- paste0(dir,"/scGate_models-master/human/generic/Bcell_scGate_Model.tsv")
master.path <- paste0(dir,"/scGate_models-master/human/generic/master_table.tsv")
my.model <- load_scGate_model(model.path, master.path)
my.model

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