evanverse (version 0.4.0)

download_geo_data: Download GEO Data Resources

Description

Downloads GEO (Gene Expression Omnibus) datasets including expression data, supplemental files, and platform annotations with error handling and logging.

Usage

download_geo_data(
  gse_id,
  dest_dir,
  overwrite = FALSE,
  log = TRUE,
  log_file = NULL,
  retries = 2,
  timeout = 300
)

Value

A list with components:

gse_object

ExpressionSet object with expression data and annotations

supplemental_files

Paths to downloaded supplemental files

platform_info

Platform information (platform_id, gpl_files)

meta

Download metadata (timing, file counts, etc.)

Arguments

gse_id

Character. GEO Series accession ID (e.g., "GSE12345").

dest_dir

Character. Destination directory for downloaded files.

overwrite

Logical. Whether to overwrite existing files (default: FALSE).

log

Logical. Whether to create log file (default: TRUE).

log_file

Character or NULL. Log file path (auto-generated if NULL).

retries

Numeric. Number of retry attempts (default: 2).

timeout

Numeric. Timeout in seconds (default: 300).

Details

Downloads GSEMatrix files, supplemental files, and GPL annotations. Includes retry mechanism, timeout control, and logging. Requires: GEOquery, Biobase, withr, cli.

References

https://www.ncbi.nlm.nih.gov/geo/

Barrett T, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Holko M, Yefanov A, Lee H, Zhang N, Robertson CL, Serova N, Davis S, Soboleva A. NCBI GEO: archive for functional genomics data sets--update. Nucleic Acids Res. 2013 Jan; 41(Database issue):D991-5.

Examples

if (FALSE) {
# Download GEO data (requires network connection):
result <- download_geo_data("GSE12345", dest_dir = tempdir())

# Advanced usage with custom settings:
result <- download_geo_data(
  gse_id = "GSE7305",
  dest_dir = tempdir(),
  log = TRUE,
  retries = 3,
  timeout = 600
)

# Access downloaded data:
expr_data <- Biobase::exprs(result$gse_object)
sample_info <- Biobase::pData(result$gse_object)
feature_info <- Biobase::fData(result$gse_object)
}