Annotate putative enhancers with functional database overlaps

Cross-references putative enhancers against all functional databases (FANTOM5, UCNEs, Regulome Active, Regulome Super, etc.) loaded in the epiRomics database. Adds boolean overlap columns for each database, a count of overlapping databases, and a novel flag for enhancers not found in any known database.

Usage

annotate_enhancers(putative_enhancers, database)

Arguments

putative_enhancers

data.frame. Output from find_putative_enhancers.

database

An epiRomics S4 database object.

Value

The input data.frame with additional columns:

overlap_<name>

Logical. TRUE if putative enhancer overlaps the named functional database (one column per database).

n_databases

Integer. Count of functional databases overlapping.

novel

Logical. TRUE if no functional database overlap (completely novel enhancer call).

Examples

db <- make_example_database()
pe <- find_putative_enhancers(db)
#> 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
pe_annot <- annotate_enhancers(pe, db)
#>   fantom: 2 / 7 (28.6%) overlap
#> Functional annotation: 2 validated (28.6%), 5 novel (71.4%)
#>   Database overlap distribution: 0 DBs=5, 1 DBs=2
table(pe_annot$novel)
#> 
#> FALSE  TRUE 
#>     2     5