MSpecificCoxPh: Metabolite by metabolite Cox proportional analysis

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

Description

The Function fits cox proportional hazard model and does classification for each metabolite

Usage

MSpecificCoxPh(
  Survival,
  Mdata,
  Censor,
  Reduce = FALSE,
  Select = 15,
  Prognostic = NULL,
  Quantile = 0.5
)

Arguments

Survival	A vector of survival time with length equals to number of subjects
Mdata	A large or small metabolic profile matrix. A matrix with metabolic profiles where the number of rows should be equal to the number of metabolites and number of columns should be equal to number of patients.
Censor	A vector of censoring indicator
Reduce	A boolean parameter indicating if the metabolic profile matrix should be reduced, default is TRUE and larger metabolic profile matrix is reduced by supervised pca approach and first pca is extracted from the reduced matrix to be used in the classifier.
Select	Number of metabolites (default is 15) to be selected from supervised PCA. This is valid only if the argument Reduce=TRUE
Prognostic	A dataframe containing possible prognostic(s) factor and/or treatment effect to be used in the model.
Quantile	The cut off value for the classifier, default is the median cutoff

Details

This function fits metabolite by metabolite Cox proportional hazard model and perform the classification based on a specified quantile. Risk score will be been estimated using a single metabolite. Function is useful for majority vote classification method and metabolite by metabolite analysis and also for top K metabolites.

Value

A object of class ms is returned with the following values

Result	The cox proportional regression result for each metabolite
HRRG	The hazard ratio statistics (Hazard-ratio, Lower confidence interval and upper confidence interval) of the riskgroup based on the riskscore and the cut off value for each metabolite
Group	The classification of the subjects based on each metabolite analysis
Metnames	The names of the metabolites for the analysis

Author(s)

Olajumoke Evangelina Owokotomo, [e-mail]

Ziv Shkedy

See Also

coxph, EstimateHR

Examples

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

## USING THE FUNCTION
Example1 = MSpecificCoxPh(Survival = Data$Survival,
Mdata = t(Data$Mdata), Censor = Data$Censor, Reduce = FALSE,
Select = 15,Prognostic = Data$Prognostic, Quantile = 0.5)

## KNOWLING THE CLASS OF THE OUTPUT
class(Example1)

## EXTRACTING THE COMPONENT OF THE FUNCTION
### HAZARD RATIO INFORMATION FOR EACH METABOLITES
Example1@HRRG

### COX MODEL RESULT FOR EACH METABOLITES
Example1@Result

### CLASSIFICATION FOR EACH METABOLITES
Example1@Group

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