impute {MOFA2} | R Documentation

## Impute missing values from a fitted MOFA

### Description

This function uses the latent factors and the loadings to impute missing values.

### Usage

    impute(
      object,
      views = "all",
      groups = "all",
      factors = "all",
      add_intercept = TRUE
    )

### Arguments

`object` | a `MOFA` object.
`views` | character vector with the view name(s), or numeric vector with view index(es).
`groups` | character vector with the group name(s), or numeric vector with group index(es).
`factors` | character vector with the factor names, or numeric vector with the factor index(es). response:gives mean for gaussian and poisson and probabilities for bernoulli. link: gives the linear predictions. inRange: rounds the fitted values from "terms" for integer-valued distributions to the next integer (default).
`add_intercept` | add feature intercepts to the imputation (default is TRUE).

### Details

MOFA generates a denoised and condensed low-dimensional representation of the data that captures the main sources of heterogeneity of the data. This representation can be used to reconstruct the data, simply using the equation `Y = WX`. For more details read the supplementary methods of the manuscript.
Note that with `impute` you can only generate the point estimates (the means of the posterior distributions). If you want to add uncertainity estimates (the variance) you need to set `impute=TRUE` in the training options. See `get_default_training_options`.

### Value

This method fills the `imputed_data` slot by replacing the missing values in the input data with the model predictions.

### Examples

    # Using an existing trained model on simulated data
    file <- system.file("extdata", "model.hdf5", package = "MOFA2")
    model <- load_model(file)

    # Impute missing values in all data modalities
    imputed_data <- impute(model, views = "all")

    # Impute missing values in all data modalities using factors 1:3
    imputed_data <- impute(model, views = "all", factors = 1:3)

[Package MOFA2 version 1.0.1 Index]