getContactFrequency

Retrieve contact frequency from .hic file using strawR package.

Identifies chromatin interaction modules by constructing a Hi-C contact network based on statistically significant interactions, followed by network clustering. The method enables comparison of module connectivity across two Hi-C datasets and is capable of detecting cell-type-specific regulatory modules. By integrating network analysis with chromatin conformation data, this approach provides insights into the spatial organization of the genome and its functional implications in gene regulation. Author: Sora Yoon (2025) <https://github.com/ysora/HiCociety>.

Sora Yoon

HiCociety

Inferring Chromatin Interaction Modules from 3C-Based Data

getContactFrequency function

<dl><dt>fname</dt>
<dd>.hic data for any types of genome conformation capture data</dd>
<dt>chr</dt>
<dd>Chromosome number of network extraction</dd>
<dt>resol</dt>
<dd>DNA basepair Resolution. Default=10000</dd></dl>

Arguments

Author

Get contact Frequency — getContactFrequency

<dl>

<dt>fname</dt>
<dd>.hic data for any types of genome conformation capture data</dd>


<dt>chr</dt>
<dd>Chromosome number of network extraction</dd>


<dt>resol</dt>
<dd>DNA basepair Resolution. Default=10000</dd>

</dl>

getContactFrequency: Get contact Frequency

Description

Usage

Value

Arguments

Author

Details

Examples