Exploring RV-NPL with simulated family data¶

Overview¶

This page includes the work processes for the simulation analysis for RV-NPL.

The workflow contains the simulation processes for families with either qualitative or quantitative traits, each contains the following 3 steps:

1. generating simulated genotypes for families with given affection status

2. using RV-NPL to generate CHP regional markers

3. performing RV-NPL analysis on families with CHP genotypes

Setting up prerequisites¶

SOS and docker need to be installed in your machine before the workflow can be performed.

Instructions on the installation can be found at: http://statgen.us/lab-wiki/orientation/jupyter-setup.html#sos-suite

Quick Trial¶

First, download the git repository:

git clone https://github.com/statgenetics/rvnpl-notes.git
cd rvnpl-notes

Then, use docker to pull the docker image for this practice:

docker pull statisticalgenetics/rvnpl
docker pull statisticalgenetics/rarepedsim

Next, try the default command below to run the workflow:

sos run analysis/NPL_Simulation.ipynb simulate

or for families with quantitative traits:

sos run analysis/QNPL_Simulation.ipynb simulate

More details on the workflow steps and the parameters can be found in the notebook analysis/NPL_Simulation.ipynb or analysis/QNPL_Simulation.ipynb.