Extract BEDPE interactions from a Hi-C matrix

Extract BEDPE interactions from a Hi-C matrix

calcApa(
  bedpe,
  hic,
  norm = "NONE",
  res = 10000,
  buffer = 5,
  filter = FALSE,
  matrix = "observed"
)

Arguments

bedpe

data.frame or data.table in BEDPE format.

hic

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.

filter

TRUE or FALSE (default). If TRUE, filterBedpe() will be used to remove short intrachromosomal interactions that would otherwise cross the diagonal.

matrix

Type of matrix to output. Can be one of observed/oe/expected. observed is observed counts, oe is observed/expected counts, expected is expected counts.

Value

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