get_variance_explained: Get variance explained values

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

Get variance explained values

Description

Extract the latent factors from the model.

Usage

get_variance_explained(
  object,
  groups = "all",
  views = "all",
  factors = "all",
  as.data.frame = FALSE
)

Arguments

object	a trained MOFA object.
groups	character vector with the group name(s), or numeric vector with the group index(es). Default is "all".
views	character vector with the view name(s), or numeric vector with the view index(es). Default is "all".
factors	character vector with the factor name(s), or numeric vector with the factor index(es). Default is "all".
as.data.frame	logical indicating whether to return a long data frame instead of a matrix. Default is FALSE.

Value

A list of data matrices with variance explained per group or a data.frame (if as.data.frame is TRUE)

Examples

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

# Fetch variance explained values (in matrix format)
r2 <- get_variance_explained(model)

# Fetch variance explained values (in data.frame format)
r2 <- get_variance_explained(model, as.data.frame = TRUE)

bioFAM/MOFA2 documentation built on June 12, 2024, 3:57 p.m.