importAndSimplifyHMM: import and simplify a REMC or ENCODE ChromHMM track

In ttriche/chromophobe: Explore genomic state models, predictions, sample compositions & overlaps

import and simplify a REMC or ENCODE ChromHMM track

Description

import and simplify a REMC or ENCODE ChromHMM track

Usage

importAndSimplifyHMM(
  x,
  genome = "mm10",
  species = NULL,
  cols = NULL,
  verbose = FALSE,
  ...
)

Arguments

x	a BED filename with a ChromHMM segmentation in it
genome	a genome associated with the segmentation (default is mm10)
species	a species for the segmentation (default: guess from genome)
cols	a color key for simplifying ChromHMMs (pass to simplifyHMM)
verbose	be verbose? (FALSE)
...	arguments ('only3', 'BPPARAM') for aggregateStates

Value

a GRanges of aggregated, simplified HMM states

ttriche/chromophobe documentation built on Oct. 14, 2024, 11:59 a.m.