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Tutorial Session #1: Lassosum

In this session, we are going to construct polygenic risk score using Lassosum.
References : Lassosum github, Lassosum paper.
The data we are going to use are already preprocessed or downloaded.

0. Log in to leelabguest

ssh leelabguest@147.47.200.131 -p 22555

1. Connect to CPU

ssh leelabsg[01-07]

2. Activate conda environment

conda activate r_env

3. Make directory for practice session in your directory

mkdir /data/home/leelabguest/PRS_tutorial/YOUR_DIRECTORY

4. Copy the lassosum_script.R from the PRS_tutorial/lassosum folder

cp /data/home/leelabguest/PRS_tutorial/lassosum/lassosum_script.R /data/home/leelabguest/PRS_tutorial/YOUR_DIRECTORY

5. Read lassosum_script.R using nano and change YOUR_DIRECTORY using ^o(overwrite) and ^x(exit)

nano /data/home/leelabguest/PRS_tutorial/YOUR_DIRECTORY/lassosum_script.R

6. Run lassosum

nohup Rscript /data/home/leelabguest/PRS_tutorial/YOUR_DIRECTORY/lassosum_script.R > /data/home/leelabguest/PRS_tutorial/YOUR_DIRECTORY/nohup.out &

*Way to check whether the code is running properly

ps

cat /data/home/leelabguest/PRS_tutorial/YOUR_DIRECTORY/nohup.out

7. Move to your directory

cd /data/home/leelabguest/PRS_tutorial/YOUR_DIRECTORY

8. Check the result from R

R

v <- readRDS("v.RDS")
result <- v[["results.table"]]
result