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Download RNA-seq data from GDC

Source: R/01_data_acquisition.R
download_gdc_rnaseq.Rd

Downloads RNA-seq gene expression data from the Genomic Data Commons (GDC) for the specified project. Data is saved as a SummarizedExperiment RDS and as parquet files (counts, sample metadata, gene metadata).

Usage

download_gdc_rnaseq(
  project_id = "MMRF-COMMPASS",
  data_dir = "data/raw/gdc",
  sample_limit = 200,
  random_sample = TRUE,
  seed = 42,
  use_parquet = TRUE
)

Arguments

project_id

Project identifier (default: "MMRF-COMMPASS")

data_dir

Directory to save data

sample_limit

Maximum number of samples (NULL for all, default 200)

random_sample

If TRUE and sample_limit is set, randomly sample patients using seed for reproducibility (default TRUE)

seed

Random seed for reproducible sampling (default 42)

use_parquet

If TRUE, also save parquet files alongside RDS (default TRUE)

Value

Path to the saved RDS file containing the SummarizedExperiment

See also

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

Examples

if (FALSE) { # \dontrun{
# Download 200 random samples with parquet output
rnaseq_file <- download_gdc_rnaseq(sample_limit = 200)

# Load the SummarizedExperiment
se_data <- readRDS(rnaseq_file)

# Or load parquet directly
counts <- arrow::read_parquet("data/raw/gdc/rnaseq_counts.parquet")
} # }