MetFreq: Frequency of Selected Metabolites from the LASSO, Elastic-net...

In MetabolicSurv: A Biomarker Validation Approach for Classification and Predicting Survival Using Metabolomics Signature

Description

The function selects the frquency of selection from the shrinkage method (LASSO, Elastic-net) based on cross validation, that is the number of times each metabolite occur during the cross-validation process. In case of large metabolomic matrix then the N argument can be used to select metabolites occurence at a particular frequency.

Usage

MetFreq(Object, TopK = NULL, N = 3)

Arguments

Object	An object of class cvle returned from the function CVLasoelacox.
TopK	The number of Top K metabolites (5 by default) to be displayed in the frequency of selection graph.
N	The metqbolites with the specified frequency should be displayed in the frequency of selection graph.

Details

This function outputs the mostly selected metabolites during the LASSO and Elastic-net cross validation. Selected top metabolites are ranked based on frequency of selection and also a particular frequency cqn be selected. In addition, it visualizes the selected top metabolites based on the minimum frequency specified.

Value

A vector of metabolites and their frequency of selection. Also, a graphical representation is displayed.

Author(s)

Olajumoke Evangelina Owokotomo, [e-mail]

Ziv Shkedy

See Also

cvmm, coxph, EstimateHR,CVLasoelacox

Examples

## FIRSTLY SIMULATING A METABOLIC SURVIVAL DATA
Data = MSData(nPatients = 100, nMet = 150, Prop = 0.5)

## CROSS-VALIDATION FOR LASSO AND ELASTIC-NET
Result = CVLasoelacox(Survival = Data$Survival,
Censor = Data$Censor, Mdata = t(Data$Mdata),
Prognostic = Data$Prognostic, Quantile = 0.5,
Metlist = NULL,Standardize = TRUE, Reduce=FALSE, Select=15,
Alpha = 1,Fold = 4,Ncv = 10,nlambda = 100)

## CONFIRMING THE CLASS
class(Result)

## USING THE FUNCTION
MetFreq(Result,TopK = 5, N=5)

MetabolicSurv documentation built on June 11, 2021, 9:06 a.m.