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
Returns
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
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.
Examples
## FIRSTLY SIMULATING A METABOLIC SURVIVAL DATAData = MSData(nPatients =100, nMet =150, Prop =0.5)## USING THE FUNCTIONExample1 = 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 OUTPUTclass(Example1)## EXTRACTING THE COMPONENT OF THE FUNCTION### HAZARD RATIO INFORMATION FOR EACH METABOLITESExample1@HRRG
### COX MODEL RESULT FOR EACH METABOLITESExample1@Result
### CLASSIFICATION FOR EACH METABOLITESExample1@Group