getContactProbability: Contact probability

In HiCociety: Inferring Chromatin Interaction Modules from 3C-Based Data

Contact probability

Description

It estimates contact probability based on the distance of a pair of a loci.

Usage

getContactProbability(
  tab,
  farthest = 2e+06,
  resol = 10000,
  prob,
  n_cores = NULL
)

Arguments

tab	Output from getContactFrequency function.
farthest	Maximum 1-D distance to search. Default=2Mb
resol	Hi-C resolution for test. Default = 10000
prob	Significance cutoff for negative binomial distribution. Default =0.975
n_cores	The number of cores used for parallel computing. If set as NULL, n_cores is automatically set to the number of cores in the computer if it is not exceed 30. If it is more than 30, it is set as 30. Default = NULL

Details

Get Contact probablity

Value

A list containing three objects: AREA, original, and len1, representing the statistical significance of each chromatin interaction pair.

Author(s)

Sora Yoon, PhD

Examples

# This example might take a long time to run, so we wrap it in donttest{}

myhic = system.file('extdata','example.hic',package = 'HiCocietyExample')
mydf=getContactFrequency(myhic, 19, 5000);
myprob=getContactProbability(mydf,farthest=2000000, resol=5000,prob=0.975,
n_cores=2);

HiCociety documentation built on Feb. 16, 2026, 5:10 p.m.