jrSiCKLSNMF (version 1.2.3)

SetLambdasandRowReg: Set lambda values and type of row regularization for an object of class SickleJr

Description

Provide the values for the graph regularization \(\lambda_{\textbf{W}^v}\) for each modality as a list, provide the value for the sparsity constraint \(\lambda_{\mathbf{H}}\), and select whether to use L2 norm regularization.

Usage

SetLambdasandRowReg(
  SickleJr,
  lambdaWlist = list(10, 50),
  lambdaH = 500,
  rowReg = "None"
)

Value

An object of class SickleJr with the lambda hyperparameter values added to its lambdaWlist and lambdaH slots and with the row regularization value added to its rowRegularization slot

Arguments

SickleJr

An object of class SickleJr

lambdaWlist

A list of graph regularization constraints for the \(\mathbf{W}^v\) matrices: defaults to 2 modalities with the RNA modality constraint equal to 10 and the ATAC modality constraint equal to 50

lambdaH

A numeric holding the sparsity constraint on \(\mathbf{H}\): defaults to 500.

rowReg

A string that is equal to "None" for no constraints on the rows of \(\mathbf{H}\) and "L2Norm" to set the L2 norms of the rows of \(\mathbf{H}\) to be equal to 1: defaults to "None"

Examples

SimSickleJrSmall<-SetLambdasandRowReg(SimSickleJrSmall,
lambdaWlist=list(10,50),lambdaH=500,rowReg="None")
SimSickleJrSmall<-SetLambdasandRowReg(SimSickleJrSmall,
lambdaWlist=list(3,15),lambdaH=0,rowReg="L2Norm")