R: A function to plots Kaplan-Meier curves stratified by a group...

pamr.plotsurvival {pamr} | R Documentation

## A function to plots Kaplan-Meier curves stratified by a group variable

### Description

A function to plots Kaplan-Meier curves stratified by a group variable

### Usage

    pamr.plotsurvival(group, survival.time, censoring.status)

### Arguments

`group` | A grouping factor
`survival.time` | Vector of survival times
`censoring.status` | Vector of censoring status values: 1=died, 0=censored

### Author(s)

Trevor Hastie,Robert Tibshirani, Balasubramanian Narasimhan, and Gilbert Chu

### Examples

    gendata<-function(n=100, p=2000){
      tim <- 3*abs(rnorm(n))
      u<-runif(n,min(tim),max(tim))
      y<-pmin(tim,u)
       ic<-1*(tim<u)
    m <- median(tim)
    x<-matrix(rnorm(p*n),ncol=n)
      x[1:100, tim>m] <-  x[1:100, tim>m]+3
      return(list(x=x,y=y,ic=ic))
    }

    # generate training data; 2000 genes, 100 samples

    junk<-gendata(n=100)
    y<-junk$y
    ic<-junk$ic
    x<-junk$x
    d <- list(x=x,survival.time=y, censoring.status=ic,
    geneid=as.character(1:nrow(x)), genenames=paste("g",as.character(1:nrow(x)),sep=
    ""))

    # train model
    a3<- pamr.train(d, ngroup.survival=2)

    #make class predictions

    yhat <- pamr.predict(a3,d$x, threshold=1.0)

    pamr.plotsurvival(yhat, d$survival.time, d$censoring.status)

[Package pamr version 1.55 Index]