calcApa: Extract BEDPE interactions from a Hi-C matrix

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

Extract BEDPE interactions from a Hi-C matrix

Description

Extract BEDPE interactions from a Hi-C matrix

Usage

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.

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