inst/doc/MOFA_example_simulated.R

In MOFA: Multi-Omics Factor Analysis (MOFA)

## ---- message=FALSE-----------------------------------------------------------
library(MOFA)

## -----------------------------------------------------------------------------
set.seed(1234)
data <- makeExampleData()
MOFAobject <- createMOFAobject(data)
MOFAobject

## -----------------------------------------------------------------------------
TrainOptions <- getDefaultTrainOptions()
ModelOptions <- getDefaultModelOptions(MOFAobject)
DataOptions <- getDefaultDataOptions()

TrainOptions$DropFactorThreshold <- 0.01

## -----------------------------------------------------------------------------
n_inits <- 3
MOFAlist <- lapply(seq_len(n_inits), function(it) {
  
  TrainOptions$seed <- 2018 + it
  
  MOFAobject <- prepareMOFA(
  MOFAobject, 
  DataOptions = DataOptions,
  ModelOptions = ModelOptions,
  TrainOptions = TrainOptions
)
  
  runMOFA(MOFAobject)
})

## -----------------------------------------------------------------------------
compareModels(MOFAlist)

## -----------------------------------------------------------------------------
compareFactors(MOFAlist)

## -----------------------------------------------------------------------------
MOFAobject <- selectModel(MOFAlist, plotit = FALSE)
MOFAobject

## -----------------------------------------------------------------------------
plotVarianceExplained(MOFAobject)

## -----------------------------------------------------------------------------
sessionInfo()