getCompartments: Contact map compartments

In js2264/cooleR: Analysing cool files in R with HiContacts

Contact map compartments

Description

Computes eigen vectors for each chromosome using cis contacts and extract chromosome compartments.

Usage

getCompartments(
  x,
  resolution = NULL,
  genome = NULL,
  chromosomes = NULL,
  neigens = 3,
  sort_eigens = FALSE,
  BPPARAM = BiocParallel::bpparam()
)

Arguments

x	A HiCExperiment object over a full genome
resolution	Which resolution to use to compute eigen vectors
genome	a BSgenome of DNAStringSet object associated with the Hi-C contact matrix.
chromosomes	character or integer vector indicating which
neigens	Numver of eigen vectors to extract
sort_eigens	Can be FALSE or one of c('Spearman', 'Pearson')
BPPARAM	BiocParallel parallelization settings

Value

A HiCExperiment object with additional eigens metadata containing the normalized eigenvectors and a new "compartments" topologicalFeatures storing A and B compartments as a GRanges object.

Examples

library(HiContacts)
full_contacts_yeast <- contacts_yeast(full = TRUE)
comps <- getCompartments(full_contacts_yeast)
metadata(comps)$eigens

js2264/cooleR documentation built on Jan. 29, 2024, 10:47 p.m.