For details of the methods, simulation, and data analysis, please visit Chapter 3 of my PhD thesis: https://dspace.library.uu.nl/handle/1874/428052

Simulation

R files:

• Training_split.R: split training and test
• cut_loading.R: hard thresholding the eigen vector of genetic data
• maf.R: plot MAF
• PCA_x.R: perform PCA on genetic data and take the first 20 PCs
• SNP_PCA.R: summarise SNP data to GPC data
• training_part(_snp).R: train O2PLS models, perform GWAS for omic-PRS on GPC data (on SNP data)
• test_part(_snp).R: compute metrics to evaluate performance of all methods (on SNP data)

sh files for executing on HPC (slurm)

• pre_run.sh: run SNP_PCA.R, PCA_x.R, cut_loading.R
• simu_datX.sh: run Training_split.R, SNP_PCA.R, prepare .ped file for GWAS
• simu_run(_snp).sh: Iterate over simulation settings, in each setting, run training_part.R, compute PRSs, and run test_part.R

Data analysis

Analysis_steps: steps for analysis, containing some plink and PRSice commands

R files:

• gly_process.R, mtb_process.R: read raw glycomics and metabolomics data and preprocess
• bmi_explore.R, db2_explore.R: preprocessing the outcome BMI, Type II diabetes
• GWAS_stats_process.R, GWAS_stats_process_bash: formatting downloaded GWAS
• overlapping_id.R: extract sample with omics and outcome, split into training and test
• combine_gene_gly: preprocess genetic and glycan data, ready for O2PLS
• SNP_PCA.R: summarise SNP data to GPC data
• gly(metb)_bmi.R: select glycan peaks/metabolites that are significantly associated with BMI
• Nr_comp_bmi.R: determine and number of components for O2PLS methods
• bmi_predict.R: performance of predicting BMI of all the methods
• O2PLS_gly(mtb)_fit_1000.R: fit O2PLS methods (without PO2PLS) on genetics and glycomics/metabolomics
• PO2PLS_gly(mtb)_fit_1000.R: fit PO2PLS on genetics and glycomics/metabolomics
• PO2PLS_fit_rx.R: investigating the impact of the number of x-specific component

sh files:

• run_Nr_comp.sh: run Nr_comp_bmi.R
• run_O2PLS.sh, run_PO2PLS.sh: run O2PLS, PO2PLS.
• run_rx.sh, rx_sbatch.sh: investigate the impact of the number of x-specific component
• run_PRS.sh, sbatch_PRS.sh: compute PRSs for each glycan