aberration_multigraph

Aberration multigraphs were introduced by Sachs et al. in 2002 as a model for chromosome aberrations¹. This project aims to study and analyze aberration multigraphs. Eventually, it is intended to apply them to model chromothripsis.

Chromothripsis is a catastrophic phenomenon where the entire genome of a person shatters into thousands of pieces and rearranges itself. It is known to occur in the case of certain types of cancers.

Setup

Installation

git clone https://github.com/siddharthsheth/aberration_multigraph
cd aberration_multigraph
pip install -e .

Pickle Patient Data

The following command saves the data for each patient as an IncompleteAMG object in pickled format at location aberration_multigraph/data/nihms_files/

python examples/patient_analysis/nihms_patient.py

Generate AMGs for a Patient

The following command recreates all possible completed AMGs for a patient using a file created in the previous section.

python examples/patient_analysis/nihms_amg.py

Footnotes

1. [Using graph theory to describe and model chromosome aberrations] (https://pubmed.ncbi.nlm.nih.gov/12385633/) ↩