get_covariates: Get sample covariates

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

Get sample covariates

Description

Function to extract the covariates from a MOFA object using MEFISTO.

Usage

get_covariates(
  object,
  covariates = "all",
  as.data.frame = FALSE,
  warped = FALSE
)

Arguments

object	a MOFA object.
covariates	character vector with the covariate name(s), or numeric vector with the covariate index(es).
as.data.frame	logical indicating whether to output the result as a long data frame, default is FALSE.
warped	logical indicating whether to extract the aligned covariates

Value

a matrix with dimensions (samples,covariates). If as.data.frame is TRUE, a long-formatted data frame with columns (sample,factor,value)

Examples

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

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