get.reference.maps: Retrieve and load reference atlas

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

Retrieve and load reference atlas

Description

Download and load reference atlases.

Usage

get.reference.maps(
  collection = NULL,
  reference = NULL,
  update = FALSE,
  directory = "./ProjecTILs_references",
  as.list = TRUE,
  verbose = TRUE
)

Arguments

collection	Collection to download and load. See available collection using list.reference.maps. If NULL, all are downloaded and loaded (default)
reference	References to download and load. See available collection using list.reference.maps. If NULL, all are downloaded and loaded (default)
update	Boolean whether to delete current reference maps and download them again
directory	Directory where to download and load from reference maps. By default a directory named "ProjecTILs_references" is created in working directory.
as.list	Boolean whether to simplify list (FALSE) or, by default, keep a list of lists for each collection (TRUE).
verbose	Inform of the status of processes

Examples

# explore available reference maps
list.reference.maps()

# consider increasing downloading timeout
options(timeout = 1000)

# get all available reference maps
ref.maps <- get.reference.maps()

# get certain collections or reference maps
# all human references maps
ref.maps.human <- get.reference.maps(collection = "human")

# only some references
ref.maps <- get.reference.maps(reference = "DC")
ref.maps.CD4 <- get.reference.maps(reference = c("CD4", "Virus_CD4T"))

# update previously downloaded maps
ref.maps <- get.reference.maps(update = TRUE)

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