HiCociety (version 0.1.39)

getContactProbability: 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
)

Value

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

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

Author

Sora Yoon, PhD

Details

Get Contact probablity

Examples

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