Function reference • MOSTWAS

Prior to TWAS Functions for file formatting and eQTL analysis
`convertToDosage()`	Train and predict gene's predictive model with mediators
`eQTL_MOSTWAS()`	LD prune a genotype matrix
`mergeFinalModels()`	Output final MOSTWAS models
MOSTWAS modeling Main wrapper functions for MOSTWAS expression models
`trainLocalModel()`	Train a local-only model for a phenotype
`MeTWAS()`	Train and predict gene's predictive model with mediators using MeTWAS
`DePMA()`	Train and predict gene's predictive model with mediators using DePMA
Association testing Functions for TWAS association testing
`burdenTest()`	Compute weighted burden test
`addedLastTest()`	Compute weighted burden test
Simulation framework Functions for running simulation analysis
`regress()`	Generate summary statistics for genotype-trait association
`simBeta()`	Simulate eQTL effect sizes
`simEQTL()`	Simulate eQTL reference panel
`simGeno()`	Simulate genotypes from reference data
`simGWAS()`	Simulate eQTL reference panel
`simTrait()`	Simulate trait from latent genetic values
Miscellaneous Functions used internally in MOSTWAS
`adjR2()`	Compute McNemar's adjusted R2
`amplifyTrans()`	Write out mediator-based trans-eSNP effects
`computeTME()`	Compute total mediation effect
`CVFitMediator()`	Fit a single split in cross-validation for a given biomarker
`estimateHeritability()`	Estimate germline heritability of a biomarker
`gatherMediators()`	Extract mediating biomarkers for a given gene
`getCisGenotypes()`	Gather the cis-genotypes for a given biomarker
`LDprune()`	LD prune a genotype matrix
`permuteTME()`	Perform permutation test for the total mediation effect
`RepParallel()`	Parallel implementation of replicate()
`sobelTest()`	Compute total mediation effect
`testTME()`	Run TME tests through a data.frame of mediators
`trainMediator()`	Train and predict mediator predictive model
`trainSNPPheno()`	Train a local-only model for a phenotype
`trainLocalModel()`	Train a local-only model for a phenotype
`trainDeP()`	Train and predict gene's predictive model with mediators using DePMA
`trainExpression()`	Train and predict gene's predictive model with mediators using MeTWAS

Reference

Prior to TWAS

MOSTWAS modeling

Association testing

Simulation framework

Miscellaneous