superpc (version 1.09)

superpc.train: Prediction by supervised principal components

Description

Does prediction of a quantitative regression or survival outcome, by the supervised principal components method.

Usage

superpc.train(data, type = c("survival", "regression"), s0.perc=NULL)

Arguments

data

Data object with components x- p by n matrix of features, one observation per column; y- n-vector of outcome measurements; censoring.status- n-vector of censoring censoring.status (1= died or event occurred, 0=survived, or event was censored), needed for

type

Problem type: "survival" for censored survival outcome, or "regression" for simple quantitative outcome

s0.perc

Factor for denominator of score statistic, between 0 and 1: the percentile of standard deviation values added to the denominator. Default is 0.5 (the median)

Value

• gene.scores=gene.scores, type=type, call = this.call
• feature.scores
  Score for each feature (gene)
• type
  problem type
• call
  calling sequence

Details

Compute wald scores for each feature (gene), for later use in superpc.predict and superpc.cv

References

Bair E, Tibshirani R (2004) Semi-supervised methods to predict patient survival from gene expression data. PLoS Biol 2004 April; 2 (4): e108; http://www-stat.stanford.edu/~tibs/superpc

Examples

#generate some example data
set.seed(332)
x<-matrix(rnorm(1000*40),ncol=40)
y<-10+svd(x[1:60,])$v[,1]+ .1*rnorm(40)
censoring.status<- sample(c(rep(1,30),rep(0,10)))

featurenames <- paste("feature",as.character(1:1000),sep="")
data<-list(x=x,y=y, censoring.status=censoring.status, featurenames=featurenames)


a<- superpc.train(data, type="survival")

Run the code above in your browser using DataCamp Workspace