The Genomic SEM software package, GenomicSEM, is written as an R package and is available through GitHub at https://github.com/MichelNivard/GenomicSEM. GenomicSEM contains several functions, including procedures for QCing and standardizing summary statistics, a function for producing genetic covariance matrices (SLDSC) and their associated sampling covariance matrices (VSLDSC) using a multivariable extension of LD Score regression, functions for fitting Genomic Structural Equation Models to SLDSC and VSLDSC, and functions for adding SNP level data to the SLDSC and VSLDSC matrices (referred to as SFull and VSFull) that are used for implementing Genomic SEM for multivariate GWAS discovery. Functions include both pre-specified models (e.g., a single common factor model) and user-specified models. Output includes both unstandardized and standardized solutions, along with the fit indices described above. WLS estimation is the default in the GenomicSEM package. GenomicSEM uses the lavaan Structural Equation Modeling package64 as the primary workhorse for model specification and numerical optimization. We also provide limited support for OpenMx.65 To run the multivariable LDSC function on five phenotypes takes ~15 minutes, a step in the analyses that only needs to be performed
