perm-class: The perm Class.

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

Description

Class of object returned by function DistHR.

Usage

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

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

## S4 method for signature 'perm,ANY'
plot(x, y, ...)

Arguments

object	A perm class object
x	A perm class object
y	missing
...	The usual extra arguments to generic functions — see plot, plot.default

Slots

HRobs

Estimated HR for low risk group on the original data.

HRperm

Estimated HR for low risk group on the permuted data

nperm

Number of permutations carried out.

Validation

The validation scheme that was used.

Note

The first, third and last vertical line on the plot are the lower, median and upper CI of the permuted data estimated HR while the red line is the estimated HR of the original data

Author(s)

Olajumoke Evangelina Owokotomo, [e-mail]

Ziv Shkedy

See Also

DistHR, EstimateHR, SurvPcaClass, SurvPlsClass, Majorityvotes, Lasoelacox, EstimateHR, Lasoelacox

Examples

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

## USING THE FUNCTION
Example <- DistHR(Survival = Data$Survival,Mdata = t(Data$Mdata),
Censor = Data$Censor,Reduce=FALSE,Select=15,Prognostic=Data$Prognostic,
Quantile = 0.5, nperm=10, case=2, Validation=c("L1based"))

## GET THE CLASS OF THE OBJECT
class(Example)     # A "perm" Class

##  METHOD THAT CAN BE USED FOR THIS CLASS
show(Example)
summary(Example)
plot(Example)

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