load.reference.map: Load Reference Atlas

In carmonalab/ProjecTILs: Reference-based analysis of scRNA-seq data

Load Reference Atlas

Description

Load or download the reference map for dataset projection. By the default it downloads a reference atlas of tumour-infiltrating lymphocytes (TILs) from mouse.

Usage

load.reference.map(ref = "referenceTIL")

Arguments

ref	Reference atlas as a Seurat object (by default downloads a mouse reference TIL atlas). To use a custom reference atlas, provide a .rds object or a URL to a .rds object, storing a Seurat object prepared using make.reference

Examples

# consider increasing downloading timeout, if downloading Default reference atlas or large reference
options(timeout = 1000)

# Download and load default reference map
ref <- load.reference.map()

# download reference map
ref.web <- load.reference.map(ref = url)

# Load any reference map
ref <- load.reference.map(ref = "path/to/ref")

carmonalab/ProjecTILs documentation built on April 13, 2025, 10:04 p.m.