Skip to contents

Generate input data for MOFA2 package

Source: R/mofa2.R
get_input_mofa2.Rd

Creates an object that can be used as input for the MOFA or MEFISTO analysis implemented in the MOFA2 package. It contains the omics datasets as well as features and samples metadata. Should not be called directly; instead use get_input_mofa or get_input_mefisto.

Usage

get_input_mofa2(
  mo_data,
  datasets,
  covariates,
  groups,
  options_list,
  only_common_samples
)

Arguments

mo_data

A MultiDataSet-class object.

datasets

Character vector, the names of the datasets from mo_data to include in the analysis.

covariates

Character or character vector of length 2, the column name(s) in the samples metadata data-frames to use as continuous covariates. if NULL, creates an input object for MOFA. If not null, creates an input object for MEFISTO.

groups

Character, the column name in the samples metadata data-frames to use as group.

options_list

A named list. Should contain at most 3 or 4 elements (depending on whether the input is for MOFA or MEFISTO), named 'data_options', 'model_options', 'training_options' and 'mefisto_options' (latter only for MEFISTO input).

only_common_samples

Logical, whether only the samples present in all datasets should be returned. Default value is FALSE.

Value

A MOFA object.