extractCounts: Extract counts from .hic file(s)

In EricSDavis/hictoolsr: An R Package for Hi-C Data Analysis

Extract counts from .hic file(s)

Description

Extract counts from .hic file(s)

Usage

extractCounts(
  bedpe,
  hic,
  chroms = c(1:22, "X", "Y"),
  res = 10000,
  norm = "NONE",
  matrix = "observed"
)

Arguments

bedpe	GInteraction object that has been binned to the correct resolution
hic	Path to .hic file
chroms	Character vector of chromosomes to extract
res	Resolution of bedpe bins
norm	string hic normalization <NONE/VC/VC_SQRT/KR>.
matrix	string matrix values to extract. Either 'observed', 'oe', or 'expected'.

EricSDavis/hictoolsr documentation built on Sept. 4, 2022, 12:36 a.m.