Aneuploidy Rates Simulation

This is a repository for the code used to produce data in the paper.

File Explanation

The data/ folder contains generated data organized by date. Below is an overview of the contents:

Folders

The main data files supporting the paper are:

• 04-04c, 04-04d, 04-04e
  Contains 3000 ABC_seq Lenormand data for Capalbo.

• 04-08c, 04-08d, 04-08e
  Contains 3000 ABC_seq Lenormand data for Munne 2017.

• 04-16c, 04-16d, 04-16e
  Contains 3000 ABC_seq Lenormand data for Walters-Sen.

• 04-18c, 04-18d, 04-18e
  Contains 3000 ABC_seq Lenormand data for Rodrigo.

• 04-19c, 04-19d, 04-19e
  Contains 3000 ABC_seq Lenormand data for Clarke.

• 04-21
  Includes misdiagnosed rates applied to expected values with dispersal levels of 0, 0.5, and 1 for Capalbo.

• 04-22
  Contains generated embryos based on distributions from 04-21.

• 07-18
  Contains generated embryos and two biopsies based on distributions from 04-04.

Usage

All shell scripts in this repository are written for computing clusters that use the SLURM job scheduler. They utilize SLURM's parallelization features to efficiently run simulations and analyses across multiple compute nodes.

Note that all the embryo create and biopsy simulation are done by functions included in the Tessera package, developed by Skinner et al.. The code is published here: Tessera

sequential_abc.R

Implements the sequential ABC algorithm, estimating posterior distributions of meiotic and mitotic error rates by comparing simulated and observed data.

seq_abc.sh

A shell script that runs the sequential ABC pipeline in sequential_abc.R.

biopsy_simulation.R

Simulates the re-biopsy process of embryos generated by posterior distribution from ABC.

run_biopsy.sh

A shell script that parallels the re-biopsy process in biopsy_simulation.R.

misdiagnosed_rates.R

Simulates misclassification of biopsies and generates datasets with the newly adjusted biopsy proportions, providing insights into the reliability of ABC inference under various conditions.

misdiagnosed_generate.sh

A shell script that runs the misdiagnosis scenarios in misdiagnosed_rates.R.

embryo_generate.R

Simulates embryo aneuploidy profiles based on specified meiotic and mitotic error rates. Generates datasets for posterior distribution analysis.

embryo_generate.sh

A shell script that runs embryo_generate.R.

plot_data.R

Generates visualizations from the simulation results for the paper.