Skip to contents

Return chromatin state category definitions

Source: R/chromatin_states.R
chromatin_state_categories.Rd

Variant of classify_chromatin_states that outputs simplified single-state categories. Resolves dual-mark states (bivalent = H3K4me3 + H3K27me3, poised = H3K4me1 + H3K27me3) to the single most likely state, useful for applications that require one-state-per-region classification.

Usage

chromatin_state_categories(
  database,
  histone_marks = NULL,
  regions = NULL,
  refine_by_tss = TRUE,
  tss_window = 2000L
)

Arguments

database

epiRomics class database containing all data initially loaded

histone_marks

character vector of histone mark names to use for classification. Must match names in meta(database). If NULL, auto-detects from meta.

regions

GRanges object of regions to classify. If NULL, uses all annotations in the database.

refine_by_tss

logical. If TRUE (default), promoter states are assigned only to regions within tss_window of an annotated TSS. Regions with promoter marks (H3K4me3) outside TSS windows are reclassified as enhancers.

tss_window

integer. Distance in bp around each TSS to define the promoter zone (default: 2000L). Regions within +/- tss_window of any annotated TSS are considered "promoter" context.

Value

data.frame with same structure as classify_chromatin_states but chromatin_state uses ChromHMM-compatible labels: active_promoter, active_enhancer, active, primed_enhancer, transcribed, polycomb_repressed, heterochromatin, quiescent, low_signal

Details

State resolution rules:

  • active_promoter: H3K4me3 + H3K27ac (replaces "active" when K4me3 present; includes former bivalent with K27ac)

  • active_enhancer: H3K4me1 + H3K27ac (distal active elements)

  • active: H3K27ac alone (sufficient per Creyghton et al. 2010)

  • primed_enhancer: H3K4me1 alone (no K27ac, no K27me3)

  • transcribed: H3K36me3 alone (SETD2/Pol II gene body mark; standard epiRomics marks this as "unmarked")

  • polycomb_repressed: H3K27me3 (Polycomb Repressive Complex; absorbs former poised and bivalent-without-K27ac)

  • heterochromatin: H3K9me3 (constitutive heterochromatin)

  • quiescent: No histone marks detected

  • low_signal: Borderline marks or H2A.Z only

Bivalent resolution: K4me3 + K27me3 + K27ac -> active_promoter (K27ac sufficient for active). K4me3 + K27me3 without K27ac -> polycomb_repressed (K27me3 dominates without activating mark).

Poised resolution: K4me1 + K27me3 -> polycomb_repressed (K27me3 dominates in single-state HMM framework).

References

Ernst J, Kellis M (2012) Nature Methods 9(3):215-216. "ChromHMM: automating chromatin-state discovery and characterization."

See also

classify_chromatin_states for the standard epiRomics classification with bivalent/poised states.

Examples

db <- make_example_database()
cats <- chromatin_state_categories(db)
table(cats$chromatin_state)
#> 
#>             active    active_enhancer    active_promoter         low_signal 
#>                  1                  1                  2                  1 
#> polycomb_repressed    primed_enhancer        transcribed 
#>                  2                  1                  2