InterDomain

InterDomain is a Python package for detecting metadomains in Hi-C contact matrices. It supports both intra-chromosomal and inter-chromosomal metadomain calling, allowing researchers to identify significant genomic interactions within and between chromosomes.

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Installation

Requirements

• Python: Version 3.6 or higher
• Dependencies: The following Python packages are required:
  • numpy
  • pandas
  • cooler
  • scipy
  • matplotlib

Installation Steps

Clone the Repository:

git clone https://github.com/yourusername/InterDomain.git
cd InterDomain
pip install .

Usage

Intra and Inter-chromosomal Metadomain Calling

• To perform intra-chromosomal metadomain calling, use the call_metadomains_intra command:
  • call_metadomains_intra path/to/your_file.cool
• To perform inter-chromosomal metadomain calling, use the call_metadomains_inter command:
  • call_metadomains_inter path/to/your_file.cool

The commands are similar for both intra and inter metadomains, with slight modifications to the hyperparameters. The following are the main arguments for both commands:

• --n_workers: Number of worker processes to use (default: 1; max: number of chromosomes).
• --label: Label for the output files (default: 'test').
• --save_intermediates: Save intermediate matrices for plotting and inspection of results (default: False).
• --useSigma: Use sigma for smoothing (intra default: False; inter default: True; recommended for sparser matrices and interchromosomal matrices).
• --sigma: Sigma value for smoothing if --useSigma is set (default: 0.75).
• --prominence: Prominence threshold for peak detection (default: 4).
• --minweight: Minimum weight for balancing (default: 0.0025).
• --pc: Pseudocount for observed/expected calculations (default: 1e-6).
• --pmin: Minimum p-value for statistical tests (default: 1e-300).
• --frac_min_valid: Minimum fraction of valid pixels for filters (default: 0).
• --filter_n: Size of the outside filter (default: 35).
• --filter_width: Size of the inside filter (intra default: 1; inter default: 3;).
• --output_dir: Directory to save output files (default: 'bedfile_output/').
• --cutoff: intra only; determines the minimum size of a metadomain (default: 2,000,000).

Outputs

Results will be saved in the specified directory (--output_dir; default: 'bedfile_output/'). The output files will contain the metadomain coordinates and other relevant information, and are saved as .tsv files. Intra and inter-chromosomal results will be saved in separate directories (/intra/ and /inter/).

Intermediate results can be saved in --save_intermediates, which can allow for better visualization of intermediate steps in the metadomain calling process.

Intermediate files are as follows:

• Observed and expected matrices
• Balanced matrices
• Smoothed matrices
• Peak detection results
• -LogP values

Plotting Metadomains

After running the metadomain calling, you can visualize the most significant metadomains using the interdomain_plot command. This command requires :

• --top_n: specify the number of metadomains to plot
• --output_dir: specify what the output dir was for your dataset
• --type: specify whether to plot intrachromosomal or interchromosomal metadomains