extracts Hi-C data from a .hic file

bb_readHic(
  hic,
  chrom,
  params = NULL,
  chromstart = NULL,
  chromend = NULL,
  resolution = "auto",
  zrange = NULL,
  norm = "KR",
  res_scale = "BP",
  dataType = "observed",
  assembly = "hg19",
  altchrom = NULL,
  altchromstart = NULL,
  altchromend = NULL
)

Arguments

hic	path to .hic file
chrom	chromosome of desired region
params	an optional "bb_params" object space containing relevant function parameters
chromstart	start position
chromend	end position
resolution	the width of each pixel; "auto" will attempt to choose a resolution (in basepairs) based on the size of the region
zrange	the range of interaction scores to plot, where extreme values will be set to the max or min; if null, zrange will be set to (0, max(data))
norm	hic data normalization; must be found in hic file
res_scale	resolution scale; options are "BP" and "FRAG"
dataType	type of data to be returned; options are "observed" and "oe"
assembly	desired genome assembly
altchrom	if looking at region between two different chromosomes, this is the specified alternative chromosome
altchromstart	if looking at region between two different chromosomes, start position of altchrom
altchromend	if looking at region between two different chromsomes, end position of altchrom

Value

Function will return a 3-column dataframe: chrom, altchrom, counts

Examples

download.file("https://www.encodeproject.org/files/ENCFF606XNW/@download/ENCFF606XNW.hic", destfile = "ENCFF606XNW.hic", method = "auto")
bb_readHic(hic = "./ENCFF606XNW.hic", chrom = "chr1")
bb_readHic(hic = "./ENCFF606XNW.hic", chrom = "chr1", chromstart = 22500000, chromend = 23200000, zrange = c(0, 125))
bb_readHic(hic = "./ENCFF606XNW.hic", chrom = "chr1", altchrom = "chr2")