Download clinical data from GDC — download_clinical_data • coMMpass

Downloads clinical and biospecimen data from the Genomic Data Commons (GDC) for the specified project. Data is saved in parquet and RDS formats.

Usage

download_clinical_data(
  project_id = "MMRF-COMMPASS",
  data_dir = "data/raw/clinical",
  use_parquet = TRUE
)

Arguments

project_id: Project identifier (default: "MMRF-COMMPASS")
data_dir: Directory to save data
use_parquet: If TRUE, also save parquet files (default TRUE)

Value

Path to the directory containing the saved data files

See also

Other data-acquisition: acquire_commpass_data(), download_gdc_rnaseq(), download_s3_subset(), get_commpass_clinical(), list_s3_commpass(), query_commpass_rna()

Examples

if (FALSE) { # \dontrun{
# Download clinical data
clinical_dir <- download_clinical_data()

# Load from parquet
clinical <- arrow::read_parquet(file.path(clinical_dir, "clinical_data.parquet"))
} # }