Extract BEDPE interactions from a Hi-C matrix

Extract BEDPE interactions from a Hi-C matrix

bb_calcApa(
  bedpe,
  hicFile,
  norm = "NONE",
  res = 10000,
  buffer = 5,
  equalLengthOut = T
)

Arguments

bedpe	data.frame or data.table in BEDPE format.
hicFile	string path to .hic file.
norm	string hic normalization <NONE/VC/VC_SQRT/KR>.
res	integer resolution of bedpe bins.
buffer	integer number of res-length bins from the center pixel.
equalLengthOut	logical can be set to false to get an APA list that is not the same length as the number of rows of the input bedpe file. Adds a slight efficieny boost.

Value

Returns a list APA matricies that can be compiled and plotted.