Fetch ChromHMM Chromatin States from Roadmap Epigenomics

Usage

FetchChromatinStates(
  model = 18,
  tissue,
  genome = c("hg19", "hg38"),
  mnemonics = TRUE,
  cache_dir = "~/.chromatic_cache",
  fuzzy_matching = TRUE
)

Arguments

model: Which ChromHMM model to use: 15, 18, or 25 states.
tissue: Either a Roadmap Epigenome ID (e.g., "E066"), a tissue mnemonic (e.g., "LNG.IMR90"), or a human-readable tissue name (e.g., "IMR90 fetal lung fibroblasts").
genome: Genome assembly: "hg19" or "hg38".
mnemonics: Logical, if TRUE returns the mnemonic states (default) instead of raw state numbers.
cache_dir: Directory to cache downloaded files.
fuzzy_matching: Logical, if TRUE allows partial/fuzzy matching with an interactive prompt.

Value

A GRanges object with ChromHMM states.