Extract counts from .hic file(s)

Extract counts from .hic file(s)

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'.