getWeights: getWeights

In bioFAM/MOFA: Multi-Omics Factor Analysis (MOFA)

Description

Extract the weights from the model.

Usage

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

Arguments

object	a trained MOFAmodel object.
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 list of matrices. Default is FALSE.

Value

By default it returns a list where each element is a loading matrix with dimensionality (D,K), where D is the number of features and K is the number of factors.
Alternatively, if as.data.frame is TRUE, returns a long-formatted data frame with columns (view,feature,factor,value).

Examples

# load a trained MOFAmodel object
filepath <- system.file("extdata", "CLL_model.hdf5", package = "MOFAdata")
MOFAobject <- loadModel(filepath)
# get weights as a list of matrices
weightList <- getWeights(MOFAobject, view = "all", factors = 1:4)
# get weights as a data.frame
head(getWeights(MOFAobject, view = "Mutations", as.data.frame = TRUE))

bioFAM/MOFA documentation built on Oct. 3, 2020, 12:53 a.m.