## ----message=FALSE------------------------------------------------------------ library(data.table) library(MOFA2) ## ----------------------------------------------------------------------------- data <- make_example_data( n_views = 2, n_samples = 200, n_features = 1000, n_factors = 10 )[[1]] lapply(data,dim) ## ----message=FALSE------------------------------------------------------------ MOFAobject <- create_mofa(data) ## ----------------------------------------------------------------------------- plot_data_overview(MOFAobject) ## ----message=FALSE------------------------------------------------------------ N = ncol(data[[1]]) groups = c(rep("A",N/2), rep("B",N/2)) MOFAobject <- create_mofa(data, groups=groups) ## ----------------------------------------------------------------------------- plot_data_overview(MOFAobject) ## ----------------------------------------------------------------------------- filepath <- system.file("extdata", "test_data.RData", package = "MOFA2") load(filepath) head(dt) ## ----------------------------------------------------------------------------- MOFAobject <- create_mofa(dt) print(MOFAobject) ## ----out.width = "80%"-------------------------------------------------------- plot_data_overview(MOFAobject) ## ----------------------------------------------------------------------------- data_opts <- get_default_data_options(MOFAobject) head(data_opts) ## ----------------------------------------------------------------------------- model_opts <- get_default_model_options(MOFAobject) model_opts$num_factors <- 10 head(model_opts) ## ----------------------------------------------------------------------------- train_opts <- get_default_training_options(MOFAobject) head(train_opts) ## ----message=FALSE------------------------------------------------------------ MOFAobject <- prepare_mofa( object = MOFAobject, data_options = data_opts, model_options = model_opts, training_options = train_opts ) ## ----------------------------------------------------------------------------- outfile = file.path(tempdir(),"model.hdf5") MOFAobject.trained <- run_mofa(MOFAobject, outfile, use_basilisk=TRUE) ## ----------------------------------------------------------------------------- sessionInfo()