Package index • gsemr

Genetic covariance (LDSC)

Estimate the genetic covariance structure from GWAS summary statistics.

ldsc(): Run LD Score Regression
s_ldsc(): Stratified LD Score Regression
hdl(): High-Definition Likelihood Estimation
convert_hdl_panels(): Convert HDL LD Reference Panels to Text Format

Summary-statistic preparation

QC and harmonise raw GWAS files before LDSC / multivariate GWAS.

munge(): Munge GWAS Summary Statistics
sumstats(): Merge GWAS Summary Statistics

Structural equation models

Fit factor models to the genetic covariance structure.

commonfactor(): Fit Common Factor Model
usermodel(): Fit a User-Specified SEM Model
write.model(): Auto-Generate Model Syntax from Factor Loadings
rgmodel(): Model-Implied Genetic Correlation Matrix

Multivariate GWAS

Fit a SEM at every SNP (or gene) in a merged sumstats file.

commonfactorGWAS(): Run Common Factor GWAS
userGWAS(): Run User-Specified GWAS
multiSNP(): Multi-SNP Joint Analysis
multiGene(): Multi-Gene Joint Analysis

Diagnostics and downstream analyses

paLDSC(): Parallel Analysis on LDSC Results
enrich(): Enrichment Analysis
summaryGLS(): Generalized Least Squares
simLDSC(): Simulate GWAS Summary Statistics