fcv-class: The fcv Class.

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

Description

Class of object returned by function Icvlasoel.

Usage

## S4 method for signature 'fcv'
show(object)

## S4 method for signature 'fcv'
summary(object)

## S4 method for signature 'fcv,missing'
plot(x, y, type = 1, ...)

Arguments

object	A fcv class object
x	A fcv class object
y	missing
type	Plot type. 1 is the distribution of the inner cross validated HR under test data for each outer iterations and estimated HR on the out of bag data are superimposed. 2 Estimated HR Density for low Risk Group .
...	The usual extra arguments to generic functions — see plot, plot.default

Slots

Runtime

A vector of runtime for each iteration measured in seconds.

Fold

Number of folds used.

Ncv

Number of outer cross validations used.

Nicv

Number of inner cross validations used.

TopK

The Top metabolites used

HRInner

A 3-way array in which first, second, and third dimensions correspond to Nicv, 1, and Ncv respectively. This contains estimated HR for low risk group on the out of bag data.

HRTest

A matrix of survival information for the test dataset based on the out of bag data. It has three columns representing the estimated HR, the 95% lower confidence interval and the 95% upper confidence interval.

Weight

A matrix with columns equals number of TopK metabolites and rows Ncv. Note that Weights are estimated as colMeans of coefficients matrix return from the inner cross validations.

Author(s)

Olajumoke Evangelina Owokotomo, [e-mail]

Ziv Shkedy

See Also

CVLasoelacox, EstimateHR, glmnet, Lasoelacox

Examples

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

## USE THE FUNCTION
Eg = Icvlasoel(Data$Survival, Data$Censor, Data$Prognostic,
t(Data$Mdata), Fold = 3,Ncv = 5, Nicv = 7, Alpha = 1,
TopK = colnames(Data$Mdata[,80:100]), Weights = FALSE)

## GET THE CLASS OF THE OBJECT
class(Eg)     # An "fcv" Class

##  METHOD THAT CAN BE USED FOR THIS CLASS
show(Eg)
summary(Eg)
plot(Eg, type =1)

OlajumokeEvangelina/MetabolicSurv documentation built on Aug. 7, 2019, 1:06 p.m.