Title: Modeling the genomic architecture of adiposity and anthropometrics across the lifespan
Priprint on medRxiv:
https://doi.org/10.1101/2024.08.14.24312003
GenomicSEM_efa_cfa_multivariateGWAS.sh
A vignette-style script including code used to:
- wrangle the input GWAS summary statistics
- perform the Genomic SEM exploratory factor analysis (EFA)
- perform the Genomic SEM confirmatory factor analysis (CFA)
- perform the multivariate GWAS for the 4 factors
DrugGeneNetworks.R
An R script that was used to:
- construct the drug-gene networks
- make the plots to visualize the network
PheWAS_Results.R
An R script that was used to:
- plot the phewas associations
Implementation of Genomic SEM to perform the EFA, CFA, and genetic correlations was based on the software wiki:
https://github.com/GenomicSEM/GenomicSEM/wiki
Implementation of LDpred2 to derive PRS weights followed the software vignette:
https://privefl.github.io/bigsnpr/articles/LDpred2.html
Implementation of DEPICT to analyze the multivariate GWAS followed the software readme:
https://github.com/perslab/depict
Implementation of FOCUS to perform TWAS analysis followed the software wiki: