Run MOFA2

Source: R/run_mofa2.R

Run Multi-Omics Factor Analysis v2 (MOFA2).

run_mofa2(
  mat_list,
  groups = NULL,
  metadata = NULL,
  metadata_idcol = "sample",
  transpose = FALSE,
  maxiter = 1000,
  data_options = NULL,
  model_options = NULL,
  training_options = NULL,
  stochastic_options = NULL,
  mefisto_options = NULL,
  outfile = file.path(tempdir(), "model.hdf5"),
  reductions = c("umap"),
  seed = 2020,
  verbose = TRUE,
  ...
)

Arguments

mat_list

Named list of input data matrices.
groups

group information, only relevant when using the multi-group framework.
transpose

First transpose each matrix in mat_list.
maxiter

Maximum number of training iterations (DEFAULT = 1000).
outfile

output file for the model (.hdf5 format). If NULL, a temporary file is created.
reductions

In addition to returning MOFA factors, further reduce the data with "umap" and/or "tsne".
seed

Seed passed to \[base]set.seed for reproducibility between runs.
verbose

Print messages.
...

Additional parameters passed to run_mofa.

Source

MOFA2 site

Details

Uses run_mofa to reduce a single dataset, or multiple views of the same dataset, into a set number of factors.