Generate MEFISTO input data — get_input

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

Usage

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

Arguments

mo_data: A MultiDataSet-class object.
covariates: Character or character vector of length 2, the column name(s) in the samples metadata data-frames to use as continuous covariates.
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).
options_list: A named list. Should contain at most 4 elements, named 'data_options', 'model_options', 'training_options' and 'mefisto_options'. Provide respectively the data, model, training and mefisto options to apply for the MEFISTO run. See get_default_data_options, get_default_model_options, get_default_training_options and get_default_mefisto_options.
only_common_samples: Logical, whether only the samples present in all datasets should be returned. Default value is FALSE.

Value

A MOFA object.