cvsim-class function

class

The cvsim Class.

Slots

• HRpca: A 3-way array in which first, second, and third dimensions correspond to number of metabolites, Hazard ratio infromation(Estimated HR, LowerCI and UpperCI), and number of cross validation respectively. This contains the estimated HR on test data and dimension reduction method is PCA.
• HRpls: A 3-way array in which first, second, and third dimensions correspond to number of metabolites, Hazard ratio infromation(Estimated HR, LowerCI and UpperCI), and number of cross validation respectively. This contains the estimated HR on test data and dimension reduction method is PLS.
• Nmets: The number of metabolites in the reduced matrix
• Ncv: The number of cross validation done
• Top: A sequence of top k metabolites considered. Default is Top=seq(5,100,by=5)

Examples

## GENERATE SOME METABOLIC SURVIVAL DATA WITH PROGNOSTIC FACTORS
Data<-MSData(nPatients=100,nMet=150,Prop=0.5)

## FIRST IS THE NETABOLITE BY METABOLITE ANALYSIS
w = CVMetSpecificCoxPh(Fold=3,Survival=Data$Survival,
Mdata=t(Data$Mdata),Censor= Data$Censor,Reduce=TRUE,
Select=150,Prognostic=Data$Prognostic,Quantile = 0.5,Ncv=3)

## USING THE FUNCTION
Result = CVSimet(w, Top = seq(5, 100, by = 5), Survival=Data$Survival,
 Censor=Data$Censor, Prognostic = Data$Prognostic)

## GET THE CLASS OF THE OBJECT
class(Result)     # A "cvsim" Class

##  METHOD THAT CAN BE USED FOR THE RESULT
show(Result)
summary(Result)
plot(Result, type =2)

See Also

CVPcaPls, SurvPcaClass, SurvPlsClass

Author(s)

Olajumoke Evangelina Owokotomo, olajumoke.owokotomo@uhasselt.be

Ziv Shkedy