Download a project's data files from the ScPCA Portal
Usage
download_project(
project_id,
auth_token,
destination = "scpca_data",
format = "sce",
merged = FALSE,
include_multiplexed = NULL,
overwrite = FALSE,
redownload = FALSE,
quiet = FALSE
)Arguments
- project_id
The ScPCA project ID (e.g. "SCPCP000001")
- auth_token
An authorization token obtained from
get_auth()- destination
The path to the directory where the unzipped file directory should be saved. Default is "scpca_data".
- format
The desired file format, either "sce" (SingleCellExperiment), "anndata" (AnnData/H5AD), or "spatial" (for spatial data in Space Ranger format). Default is "sce".
- merged
Download merged data files, if available. Default is FALSE.
- include_multiplexed
Include multiplexed samples, if available. Default is TRUE for SingleCellExperiment and FALSE for AnnData and spatial samples, where multiplexed data are not available.
- overwrite
Whether to overwrite files in existing directories if they already exist. Note that files in existing directories that do not have the same name as one of the downloaded files will not be deleted. Default is FALSE.
- redownload
Whether to re-download if files from the same project and format already exist. If FALSE, existing files will be returned. Default is FALSE.
- quiet
Whether to suppress download progress messages. Default is FALSE.
Examples
if (FALSE) { # \dontrun{
# Get a token first
auth_token <- get_auth("your.email@example.com", agree = TRUE)
# Then ask for a sample download
download_project("SCPCS000001", auth_token, destination = "scpca_data", format = "sce")
# Downloading merged files in AnnData format
download_project(
"SCPCS000001",
auth_token,
destination = "scpca_data",
format = "anndata",
merged = TRUE
)
} # }