# 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

```

![image](https://user-images.githubusercontent.com/6510818/136842534-32ed43ac-e80f-47b2-9788-2f5f7149d257.png)