Step 03 ‐ PRS

This step focuses on quality control of the GxAge interactions. It will evaluate the associations of externally weighted polygenic scores for the traits as positive controls. It will also generate LD matrices at each phenotype x age time point for the known variants for that phenotype. This will help to evaluate if age-differential selection bias could be driving GxAge interactions. Notes:

• This ran in about 2 minutes for 2 phenotypes in 450k samples in UKBiobank with env_threads=100 and about 10Gb RAM.

To run

./03-prs.sh

Check and archive the results

Please manually look at the $results_dir/03/ldmat directory to check that LD matrices have been generated for each age x phenotype combination available in the study. Also check that the $results_dir/03/scores.rds file is there. You may wish to inspect it in R to check that the PRS associations look as expected (e.g. scores <- readRDS("scores.rds"), which returns a data frame that has a PRS association for each age x phenotype combination).

This will generate the tarball and md5 sums for the results for this step:

./utils/archive.sh 03

Upload the results to the SFTP

./utils/upload.sh 03

(Note that this will prompt you for your SFTP password - contact us if you haven't received this.

(Optional) Running in containers

Docker

Make sure you've pulled the latest image:

docker pull mrcieu/lifecourse-gwas:latest

and then run:

./utils/run_docker.sh ./03-prs.sh

Apptainer

Make sure you've pulled the latest image:

apptainer pull docker://mrcieu/lifecourse-gwas:latest

./utils/run_apptainer.sh ./03-prs.sh