This function downloads the data files for a specified sample from the ScPCA Portal. The downloaded files are saved in a subdirectory of the specified path, named by the base filename of the downloaded zip file, which includes the sample ID, modality, format, and date.
Usage
download_sample(
sample_id,
auth_token,
destination = "scpca_data",
format = "sce",
overwrite = FALSE,
redownload = FALSE,
quiet = FALSE
)Arguments
- sample_id
The ScPCA sample ID (e.g. "SCPCS000001")
- 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".
- 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 sample and format already exist. If FALSE, existing files will be returned. Default is FALSE.
- quiet
Whether to suppress download progress messages. Default is FALSE.
Details
For single-cell and single-nuclei data, files can be downloaded in either SingleCellExperiment ("sce") or AnnData ("anndata") format, and all downloads include the unfiltered, filtered, and processed data objects, as well as associated metadata and QC files.
Spatial data, if present, can be downloaded in Space Ranger format using the "spatial" format option.
The function returns a vector of file paths for the downloaded files (invisibly).
Note that downloading data requires an authorization token, which can be obtained
using the get_auth() function.
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_sample("SCPCS000001", auth_token, destination = "scpca_data", format = "sce")
# Downloading in AnnData format
download_sample("SCPCS000001", auth_token, destination = "scpca_data", format = "anndata")
} # }