AdiposityGSEM

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:

1. wrangle the input GWAS summary statistics
2. perform the Genomic SEM exploratory factor analysis (EFA)
3. perform the Genomic SEM confirmatory factor analysis (CFA)
4. perform the multivariate GWAS for the 4 factors

DrugGeneNetworks.R

An R script that was used to:

1. construct the drug-gene networks
2. make the plots to visualize the network

PheWAS_Results.R

An R script that was used to:

1. 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:

https://github.com/mancusolab/ma-focus/wiki