Generate MOFA input data — get_input

Creates an object that can be used as input for the MOFA analysis implemented in the MOFA2 package. It contains the omics datasets as well as features and samples metadata.

Usage

get_input_mofa(
  mo_data,
  datasets = names(mo_data),
  groups = NULL,
  options_list = NULL,
  only_common_samples = FALSE
)

Arguments

mo_data: A MultiDataSet-class object.
datasets: Character vector, the names of the datasets from mo_data to include in the analysis.
groups: Character, the column name in the samples metadata data-frames to use as groups (use get_samples_metadata to view the samples metadata data-frame for each dataset). WARNING: only use if you are familiar with MOFA and its use of groups. See https://biofam.github.io/MOFA2/faq.html, section "FAQ on the multi-group functionality".
options_list: A named list. Should contain at most 3 elements, named 'data_options', 'model_options' and 'training_options'. Provide respectively the data, model and training options to apply for the MOFA run. See get_default_data_options, get_default_model_options and get_default_training_options.
only_common_samples: Logical, whether only the samples present in all datasets should be returned. Default value is FALSE.

Value

A MOFA object.