getTrainData: getTrainData

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

Description

Fetch the training data

Usage

getTrainData(object, views = "all", features = "all",
  as.data.frame = FALSE)

Arguments

object	a MOFAmodel object.
views	character vector with the view name(s), or numeric vector with the view index(es). Default is "all".
features	list of character vectors with the feature names or list of numeric vectors with the feature indices. Default is "all"
as.data.frame	logical indicating whether to return a long data frame instead of a list of matrices. Default is FALSE.

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).

Value

A list with one numeric matrix per view, containing the parsed data used to fit the MOFA model.

Examples

data("scMT_data", package = "MOFAdata")
MOFAobject <- createMOFAobject(scMT_data)
trainData_scMT <- getTrainData(MOFAobject, as.data.frame = FALSE)
(trainData_scMT[["RNA expression"]])[1:10,1:10]

data("CLL_data", package = "MOFAdata")
MOFAobject <- createMOFAobject(CLL_data)
trainData_CLL <- getTrainData(MOFAobject, as.data.frame = TRUE)
head(trainData_CLL)

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