EXPERIMENTS.md

Recreate the initial experiments

We will recreate the experiments from "Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice". The command below will download the datasets used in the mouse genome paper into a local directory called mice_data_set for processing.

Set up a Jupyter notebook with the R Kernel

Next, use the Conda package manager to set up a virtual environment to run the Jupyter notebooks that recreate the original experiments on the datasets.

conda create -n r-kernel
conda activate r-kernel
conda install r-recommended r-irkernel
conda install jupyter

Add the R-kernel spec to Jupyter and install required packages.

R -e 'IRkernel::installspec()'
R -e 'install.packages("qtl", repos = "http://cran.us.r-project.org")'
R -e 'install.packages("qqman", repos = "http://cran.us.r-project.org")'
R -e 'install.packages("data.table", repos = "http://cran.us.r-project.org")'
R -e 'install.packages("stringr", repos = "http://cran.us.r-project.org")'
R -e 'install.packages("qqman", repos = "http://cran.us.r-project.org")'
R -e 'install.packages("devtools", repos = "http://cran.us.r-project.org")'

Run Jupyter notebook

jupyter notebook

Run Map.ipynb

Running this notebook before synthesizing data is optional as the original abBMD analysis was downloaded in the steps above. Map.ipynb can be run to optinally recreate the original experiment results. To run the notebook, open ./research_paper_code/notebooks/map.ipynb in Jupyter notebook, and choose Kernel->Run All. This will run through the R-studio code in this repository that recreates the results from the original paper. As data is generated, you will see plots and data files generated in the following formats:

(base) redlined@redlined-980:~/GitHub/synthetic-data-genomics/mice_data_set/out$ head lm_abBMD_1_79646.csv
"","snp","chr","pos","p"
"1","rs29477109",11,95292217,5.05231663641996e-14
"2","rs27071351",11,96114911,7.07418067212828e-14
"3","rs27024162",11,96918116,7.17058199722633e-14
"4","rs49423067",11,96918212,7.19866140655625e-14
"5","rs29470802",11,95263588,8.04984862217419e-14
"6","rs29459746",11,95987376,1.03725122425739e-13
"7","rs50417410",11,97011284,1.04333530152468e-13
"8","rs29473466",11,96920033,1.33866242959213e-13
"9","rs221074340",11,96018255,1.35574083178291e-13