MOFA: Class to store a mofa model

MOFAR Documentation

Class to store a mofa model

Description

The MOFA is an S4 class used to store all relevant data to analyse a MOFA model

Slots

data

The input data

intercepts

Feature intercepts

samples_metadata

Samples metadata

features_metadata

Features metadata.

imputed_data

The imputed data.

expectations

expected values of the factors and the loadings.

dim_red

non-linear dimensionality reduction manifolds.

training_stats

model training statistics.

data_options

Data processing options.

training_options

Model training options.

stochastic_options

Stochastic variational inference options.

model_options

Model options.

mefisto_options

Options for the use of MEFISO

dimensions

Dimensionalities of the model: M for the number of views, G for the number of groups, N for the number of samples (per group), C for the number of covariates per sample, D for the number of features (per view), K for the number of factors.

on_disk

Logical indicating whether data is loaded from disk.

cache

Cache.

status

Auxiliary variable indicating whether the model has been trained.

covariates

optional slot to store sample covariate for training in MEFISTO

covariates_warped

optional slot to store warped sample covariate for training in MEFISTO

interpolated_Z

optional slot to store interpolated factor values (used only with MEFISTO)


bioFAM/MOFA2 documentation built on March 21, 2023, 5:27 p.m.