get_factors: Get factors

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

Get factors

Description

Extract the latent factors from the model.

Usage

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

Value

By default it returns the latent factor matrix of dimensionality (N,K), where N is number of samples and K is number of factors.
Alternatively, if as.data.frame is TRUE, returns a long-formatted data frame with columns (sample,factor,value).

Examples

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

# Fetch factors in matrix format (a list, one matrix per group)
factors <- get_factors(model)

# Concatenate groups
factors <- do.call("rbind",factors)

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

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