get_data {MOFA2} | R Documentation

## Get data

### Description

Fetch the input data

### Usage

    get_data(
      object,
      views = "all",
      groups = "all",
      features = "all",
      as.data.frame = FALSE,
      add_intercept = TRUE,
      denoise = FALSE,
      na.rm = TRUE
    )

### Arguments

`object` | a `MOFA` object.
`views` | character vector with the view name(s), or numeric vector with the view index(es). Default is "all".
`groups` | character vector with the group name(s), or numeric vector with the group index(es). Default is "all".
`features` | a *named* list of character vectors. Example: list("view1"=c("feature_1","feature_2"), "view2"=c("feature_3","feature_4")) Default is "all".
`as.data.frame` | logical indicating whether to return a long data frame instead of a list of matrices. Default is `FALSE`.
`add_intercept` | logical indicating whether to add feature intercepts to the data. Default is `TRUE`.
`denoise` | logical indicating whether to return the denoised data (i.e. the model predictions). Default is `FALSE`.
`na.rm` | remove NAs from the data.frame (only if as.data.frame is `TRUE`).

### Details

By default this function returns a list where each element is a data matrix with dimensionality (D,N) where D is the number of features and N is the number of samples.
Alternatively, if `as.data.frame` is `TRUE`, the function returns a long-formatted data frame with columns (view,feature,sample,value). Missing values are not included in the the long data.frame format by default. To include them use the argument `na.rm=FALSE`.

### Value

A list of data matrices with dimensionality (D,N) or a `data.frame` (if `as.data.frame` is TRUE)

### Examples

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

    # Fetch data
    data <- get_data(model)

    # Fetch a specific view
    data <- get_data(model, views = "view_0")

    # Fetch data in data.frame format instead of matrix format
    data <- get_data(model, as.data.frame = TRUE)

    # Fetch centered data (do not add the feature intercepts)
    data <- get_data(model, as.data.frame = FALSE)

    # Fetch denoised data (do not add the feature intercepts)
    data <- get_data(model, denoise = TRUE)

[Package MOFA2 version 1.0.1 Index]