Download and Cache epiRomics Example Data

Downloads the epiRomics example dataset (histone marks, ChIP-seq peaks, BED annotations, BigWig signal files, and differential analysis results) from a remote archive and caches it locally using BiocFileCache. Subsequent calls return the cached path without re-downloading.

Usage

cache_data(force_update = FALSE, ask = FALSE)

Arguments

force_update

Logical; if TRUE, re-download the archive even when a cached copy exists.

ask

Logical; passed to BiocFileCache::BiocFileCache(). Set to FALSE (default) for non-interactive use.

Value

A character string giving the path to the local directory containing the example data files (BigWigs, BED annotations, ChIP peaks, histones, CSV files, and template sheets).

Details

The example dataset is approximately 1.3 GB compressed and includes:

Histone/

H3K27ac, H3K4me1, H3K27me3, H3K9me3, H3K4me3, H3K36me3, and H2A.Z peak calls (BED format)

ChIP/

Transcription factor peak calls for FOXA2, MAFB, NKX2.2, NKX6.1, and PDX1 (BED format)

BED_Annotation/

FANTOM5 enhancers, UCNEs, and Human Islet Regulome active/super enhancers (BED format)

BigWigs/

ATAC-seq and RNA-seq signal tracks for human pancreatic islet alpha and beta cells (bigWig format)

CSV files

DiffBind differential accessibility results and RNA-seq differential expression results

Data are downloaded once and stored in the BiocFileCache directory (typically ~/.cache/R/BiocFileCache on Linux/macOS).

Internet requirement

The first call requires internet access to download the data archive. Subsequent calls work offline using the local cache. Use has_cache to test whether the data is already available before attempting to build vignettes or run examples.

See also

has_cache to check data availability without triggering a download.

Examples

## Check whether cached data is already available (no network).
has_cache()
#> [1] FALSE

## A lightweight toy subset is always bundled with the package and
## does not require cache_data(). Use it for quick demos:
toy_dir <- system.file("extdata", "toy", package = "epiRomics")
list.files(toy_dir)
#> [1] "BED_Annotation"                 "BigWigs"                       
#> [3] "ChIP"                           "Histone"                       
#> [5] "README.md"                      "example_epiRomics_BW_sheet.csv"
#> [7] "example_epiRomics_Db_sheet.csv" "toy_database.rds"              

# \donttest{
## Network download (~1.3 GB). Wrapped in \donttest{} per Bioconductor
## guidance. Only run interactively:
if (interactive()) {
  cache_dir <- cache_data()
}
# }