Main data acquisition function — acquire_commpass_data • coMMpass

Orchestrates the download of CoMMpass data from various sources including RNA-seq data from GDC, clinical data, and optionally AWS data.

Usage

acquire_commpass_data(
  download_rnaseq = TRUE,
  download_clinical = TRUE,
  download_aws = FALSE,
  sample_limit = 200,
  random_sample = TRUE,
  seed = 42,
  use_parquet = TRUE
)

Arguments

download_rnaseq: Whether to download RNA-seq data
download_clinical: Whether to download clinical data
download_aws: Whether to download from AWS
sample_limit: Limit number of samples (NULL for all)
random_sample: If TRUE, randomly sample patients
seed: Random seed for sampling
use_parquet: If TRUE, save parquet files

Value

List of file paths to the downloaded data

See also

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

Examples

if (FALSE) { # \dontrun{
# Download only clinical data
results <- acquire_commpass_data(
  download_rnaseq = FALSE,
  download_clinical = TRUE,
  download_aws = FALSE
)
} # }