Build a synthetic epiRomicsS4 database for use in examples

Constructs a fully populated epiRomicsS4 object from in-memory GRanges, with no network access and no external files required. The returned object contains five histone marks (h3k4me1, h3k27ac, h3k27me3, h3k4me3, h3k36me3), two ChIP-seq TF tracks (TF1, TF2), and one functional annotation track (fantom), all anchored on chr1 of hg38.

Usage

make_example_database(genome = "hg38")

Arguments

genome

Character string naming the genome assembly (default "hg38"). Only the label is changed; the synthetic GRanges are always on chr1 regardless of this value, which is sufficient for example purposes.

Value

An epiRomicsS4 object with:

annotations

GRanges containing all synthetic peak calls

meta

data.frame with columns name and type

genome

the value of genome

txdb

"TxDb.Hsapiens.UCSC.hg38.knownGene:: TxDb.Hsapiens.UCSC.hg38.knownGene"

organism

"org.Hs.eg.db"

Details

This function is the canonical data source for all @examples blocks in the epiRomics package. It is also used in vignettes and testthat helpers.

See also

make_example_putative_enhancers, make_example_enhanceosome, make_example_bigwig

Other synthetic example data helpers: make_example_bigwig(), make_example_enhanceosome(), make_example_putative_enhancers()

Examples

db <- make_example_database()
genome(db)
#> [1] "hg38"
nrow(meta(db))
#> [1] 8