Run brain mapping analyses on simulated data
by [Baptiste Couvy-Duchesne] - 13 June 2022 -
1 Create environment and output folders
wd="path/to/working/directory"
cd $wd
mkdir -p ${wd}/03_BWAS_uncorrected_allModa
mkdir -p ${wd}/09_BWAS_ICVagesex_allModa
mkdir -p ${wd}/04_BWAS_5globalPCs_allModa
mkdir -p ${wd}/05_BWAS_10globalPCs_allModa
mkdir -p ${wd}/06_BWAS_10specificPCs_allModa
mkdir -p ${wd}/07_BWAS_MOA_allModa
mkdir -p ${wd}/10_BWAS_MOA_multiORM_QC_allModa
mkdir -p ${wd}/15_BWAS_MOA_allModa_FE2 GLM no covariates
wd="path/to/working/directory"
cd ${wd}/03_BWAS_uncorrected_allModa
${wd}/qsubshcom "
for NNN in 0 10 100 1000 |;
do |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/02_phenotypesSimul/NVertices\${NNN}_Niter\${TASK_ID}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --linear --out "${wd}"/03_BWAS_uncorrected_allModa/BWAS_NVertices\${NNN}_Niter\${TASK_ID} |;
done |;
done |;
" 1 50G BWAS03_allModa 24:00:00 "-array=1-100 " 3 GLM with ICV, age and sex as covariates
cd $wd/09_BWAS_ICVagesex_allModa
${wd}/qsubshcom "
for NNN in 0 10 100 1000 |;
do |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/02_phenotypesSimul/NVertices\${NNN}_Niter\${TASK_ID}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --linear --qcovar "${wd}"/ageSexIcv.txt --out "${wd}"/09_BWAS_ICVagesex_allModa/BWAS_NVertices\${NNN}_Niter\${TASK_ID} |;
done |; " 1 50G BWAS09_allModa 24:00:00 "-array=1-100 " 4 GLM with 5 global PCs as covariates
cd ${wd}/04_BWAS_5globalPCs_allModa
${wd}/qsubshcom "
for NNN in 0 10 100 1000 |;
do |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/02_phenotypesSimul/NVertices\${NNN}_Niter\${TASK_ID}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --linear --qcovar "${wd}"/PC.5global.eigenvec --out "${wd}"/04_BWAS_5globalPCs_allModa/BWAS_NVertices\${NNN}_Niter\${TASK_ID} |;
done |;
done |;
" 1 50G BWAS04_allModa 24:00:00 "-array=1-100 " 5 GLM with 10 global PCs as covariates
cd $wd/05_BWAS_10globalPCs_allModa
${wd}/qsubshcom "
for NNN in 0 10 100 1000 |;
do |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/02_phenotypesSimul/NVertices\${NNN}_Niter\${TASK_ID}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --linear --qcovar "${wd}"/PC.10global.eigenvec --out "${wd}"/05_BWAS_10globalPCs_allModa/BWAS_NVertices\${NNN}_Niter\${TASK_ID} |;
done |;
" 1 50G BWAS05_allModa 10:00:00 "-array=1-100 " 6 GLM with 10 measurement specific PCs as covariates
cd $wd/06_BWAS_10specificPCs_allModa
${wd}/qsubshcom "
for moda in area thickness thick LogJacs |;
do |;
for NNN in 0 10 100 1000 |;
do |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.\${moda}.fwhm0.fsaverage.UKB15K --pheno "${wd}"/02_phenotypesSimul/NVertices\${NNN}_Niter\${TASK_ID}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --linear --qcovar "${wd}"/PC.10specific.\${moda}.eigenvec --out "${wd}"/06_BWAS_10specificPCs_allModa/BWAS_NVertices\${NNN}_\${moda}_Niter\${TASK_ID} |;
done |;
done |;
" 1 40G BWAS06_allModa 24:00:00 "-array=1-100 " Combine results across the different measurement types
cd $wd/06_BWAS_10specificPCs_allModa
${wd}/qsubshcom "
for NNN in 0 |;
do |;
tail -n +1 "${wd}"/06_BWAS_10specificPCs_allModa/BWAS_NVertices\${NNN}_thickness_Niter\${TASK_ID}.linear > "${wd}"/06_BWAS_10specificPCs_allModa/BWAS_NVertices\${NNN}_Niter\${TASK_ID}.linear |;
for moda in area thick LogJacs |;
do |;
tail -n +2 "${wd}"/06_BWAS_10specificPCs_allModa/BWAS_NVertices\${NNN}_\${moda}_Niter\${TASK_ID}.linear >> "${wd}"/06_BWAS_10specificPCs_allModa/BWAS_NVertices\${NNN}_Niter\${TASK_ID}.linear |;
done |;
done |;
" 1 4G BWAS_allModa_putTogether 01:00:00 "-array=1-100 " 7 LMM with global BRM
cd $wd/07_BWAS_MOA_allModa
for NNN in 0 10 100 1000
do
${wd}/qsubshcom " if [ ! -f "${wd}"/07_BWAS_MOA_allModa/BWAS_NVertices"${NNN}"_Niter\${TASK_ID}.moa ] |;
then |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/02_phenotypesSimul/NVertices"${NNN}"_Niter\${TASK_ID}.phen --orm "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC --remove "${wd}"/ID_UKB_replication.txt --moa --out "${wd}"/07_BWAS_MOA_allModa/BWAS_NVertices"${NNN}"_Niter\${TASK_ID} |;
fi " 1 60G BWAS07_${NNN}_allModa 24:00:00 "-array=1-100 "
done 8 LMM with four variance components specific to each measurement type
cd $wd/10_BWAS_MOA_multiORM_QC_allModa
for NNN in 0 10 100 1000
do
${wd}/qsubshcom "
if [ ! -f "${wd}"/10_BWAS_MOA_multiORM_QC_allModa/BWAS_NVertices"${NNN}"_Niter\${TASK_ID}.moa ] |;
then |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/02_phenotypesSimul/NVertices"${NNN}"_Niter\${TASK_ID}.phen --keep "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC.orm.id --remove "${wd}"/ID_UKB_replication.txt --moa --multi-orm "${wd}"/fwhm0.fsaverage.QC.ormlist --out "${wd}"/10_BWAS_MOA_multiORM_QC_allModa/BWAS_NVertices"${NNN}"_Niter\${TASK_ID} --reml-maxit 1000 |;
fi |;
" 1 60G BWAS10_${NNN} 48:00:00 "-array=1-100 "
done 9 LMM + covariates (ICV, age, sex)
cd $wd/15_BWAS_MOA_allModa_FE
for NNN in 0 10 100 1000
do
${wd}/qsubshcom " if [ ! -f "${wd}"/15_BWAS_MOA_allModa_FE/BWAS_NVertices"${NNN}"_Niter\${TASK_ID}.moa ] |;
then |;
"${wd}"/osca --befile "${wd}"/BodFiles/AllVertices.fwhm0.fsaverage.UKB15K --pheno "${wd}"/02_phenotypesSimul/NVertices"${NNN}"_Niter\${TASK_ID}.phen --orm "${wd}"/BodFiles/BRM.fwhm0.fsaverage.QC --remove "${wd}"/ID_UKB_replication.txt --qcovar "${wd}"/ageSexIcv.txt --moa --out "${wd}"/15_BWAS_MOA_allModa_FE/BWAS_NVertices"${NNN}"_Niter\${TASK_ID} |;
fi " 1 60G BWAS15_${NNN}_allModa 24:00:00 "-array=1-100 "
done 10 Check progress of model computation
for NNN in 0 10 100 1000
do
echo ${NNN}
ls ${wd}/03_BWAS_uncorrected_allModa/*NVertices${NNN}_*.linear | wc -l
ls ${wd}/04_BWAS_5globalPCs_allModa/*NVertices${NNN}_*.linear | wc -l
ls ${wd}/05_BWAS_10globalPCs_allModa/*NVertices${NNN}_*.linear | wc -l
ls ${wd}/06_BWAS_10specificPCs_allModa/*NVertices${NNN}_*.linear | wc -l
ls ${wd}/07_BWAS_MOA_allModa/*NVertices${NNN}_*.moa | wc -l
ls ${wd}/09_BWAS_ICVagesex_allModa/*NVertices${NNN}_*.linear | wc -l
ls ${wd}/10_BWAS_MOA_multiORM_QC_allModa/*NVertices${NNN}_*.moa | wc -l
doneA work by by [Baptiste Couvy-Duchesne] - 13 June 2022