Build a synthetic putative-enhancer result for use in examples

Returns a data.frame matching the output format of find_putative_enhancers. When database is NULL (the default), a fresh synthetic database is created internally via make_example_database and then find_putative_enhancers is called on it to produce a genuine result. This keeps the helper fast (< 2 s) while ensuring the output structure is always consistent with the real function.

Usage

make_example_putative_enhancers(database = NULL)

Arguments

database

An epiRomicsS4 object, or NULL (default). When NULL, a synthetic database is built automatically.

Value

A data.frame with columns produced by find_putative_enhancers: putative_id, chr, start, end, width, source, chromatin_state, chromatin_state_detail, histone_marks, n_histone_marks, h2az, tf_names, n_tfs.

See also

make_example_database, find_putative_enhancers

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

Examples

pe <- make_example_putative_enhancers()
#> Auto-computing chromatin states from all histone marks...
#> Histone-based enhancers: 7 regions (from 7 classified regions)
#>   States: active=4, poised=1, primed=2
#> TF binding source: 4 regions from 2 TFs (TF1, TF2)
#> Union: 7 non-overlapping putative enhancer regions
#> Putative enhancers: 7 total
#>   Active: 0 | Poised: 0 | Unmarked: 7 | Repressed: 0
#>   H2A.Z+: 0 | TF-bound: 4 | High co-binding (>=3 TFs): 0
#>   Sources: histone=3, histone,tf=4
nrow(pe)
#> [1] 7
head(pe[, c("chr", "start", "end", "chromatin_state")])
#>    chr start   end chromatin_state
#> 1 chr1  1000  2000        Unmarked
#> 2 chr1 50000 51000        Unmarked
#> 3 chr1  5000  6000        Unmarked
#> 4 chr1 20000 21000        Unmarked
#> 5 chr1 10000 11000        Unmarked
#> 6 chr1 30000 31000        Unmarked