/MS_pQTL_SMR

Primary LanguageR

Plasma proteins & MS - MR analysis

This repo contains code used to produce the results in xxx. Code by Shannon Healey and Ben Jacobs.

Data availability

  • pQTL summary statistics here
  • MS summary statistics by request here
  • SMR software here

Code

Download pQTL GWAS from UKB (https://doi.org/10.7303/syn51364943)

Setup

module load python/3.10.7
python -m venv env
source ~/env/bin/activate
python3 -m pip3 install --upgrade synapseclient

Download

module load python/3.10.7
source ~/env/bin/activate
synapse login "xxxxxx" "xxxxxx"
cd /data/scratch/hmy117/raw_ukb_pqtl_gwas
synapse get -r syn51365303

Unzip

cd /data/scratch/hmy117/raw_ukb_pqtl_gwas/
qsub ./scripts/unzip.sh

Prepare proteomics data

Get probe names

cd /data/scratch/hmy117/raw_ukb_pqtl_gwas/

# write list of files
find -type d | grep -v .tar | awk -F/ 'NR>1{print $2}' > /data/Wolfson-UKBB-Dobson/MS_pQTL_SMR/pQTLs/probe_names

Make esd directory (input for SMR)

# only run one-off as it will overwrite existing
# mkdir /data/Wolfson-UKBB-Dobson/MS_pQTL_SMR/esd_files

Get filelist with full paths to pQTL GWAS

cd /data/Wolfson-UKBB-Dobson/MS_pQTL_SMR
find /data/Wolfson-UKBB-Dobson/MS_pQTL_SMR/pQTLs -type f | grep .gz > pqtl_filelist

Make the esd files

qsub ./scripts/make_esd_files.sh

Edit epi file and make flist file in R

cd /data/Wolfson-UKBB-Dobson/MS_pQTL_SMR/
module load R/4.2.2
Rscript ./scripts/make_flist_and_epi_files.R

Make besd file

qsub ./scripts/make_besd_file.sh

Process 1kg data

Convert 1kg reference to hg38

qsub ./scripts/liftover_1kg_ref.sh

Get 1kg allele frequencies

for i in {1..22};
  do
    ~/plink2 --bfile ../1kg_reference/hg38_EUR/chr$i\_hg38 \
    --freq \
    --out ./outputs/kg_chr$i\_freq
  done

Process MS GWAS data

Rscript ./scripts/make_ma_file.R

Run SMR

qsub ./scripts/ms_smr.sh

Explore results

qsub ./scripts/explore_results.sh