get_data: Get data

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

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)

bioFAM/MOFA2 documentation built on Feb. 1, 2024, 6:41 a.m.