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run.sh
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run.sh
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#!/bin/bash
#SBATCH --time 20:00:00
#SBATCH --no-requeue
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH -p shared
ml R/3.5.1
ml parallel
set -e
## download data
bash download_data.sh
## data formatting
bash extract_protein_coding_lincRNA_genes.sh
Rscript generate_tissue_wise_TPM.R
## Learn SVs, test associations controlling for SVs
# Learn SVs - can be run in parallel
command_fn=run_SVA_compute_SV_parallel.txt
rm -f ${command_fn}
for i in {1..54}
do
echo "Rscript SVA_compute_SV_parallel.R ${i}" >> ${command_fn}
done
parallel -j 10 :::: ${command_fn}
#Rscript SVA_compute_SV.R
# Linear regression controlling for SVs
Rscript SVA_followedby_LR.R ENSG00000130234.10 ACE2
Rscript SVA_followedby_LR.R ENSG00000184012.11 TMPRSS2
## Linear regerssion controlling for known confounders
Rscript LR_confounders.R ENSG00000130234.10 ACE2
Rscript LR_confounders.R ENSG00000184012.11 TMPRSS2