superpc.listfeatures: Return a list of the important predictors

In superpc: Supervised Principal Components

Description

Return a list of the important predictor

Usage

    superpc.listfeatures(data, 
                         train.obj, 
                         fit.red, 
                         fitred.cv=NULL,
                         num.features=NULL, 
                         component.number=1)

Arguments

data	Data object
train.obj	Object returned by superpc.train
fit.red	Object returned by superpc.predict.red, applied to training set
fitred.cv	(Optional) object returned by superpc.predict.red.cv
num.features	Number of features to list. Default is all features.
component.number	Number of principal component (1,2, or 3) used to determine feature importance scores

Value

Returns matrix of features and their importance scores, in order of decreasing absolute value of importance score. The importance score is the correlation of the reduced predictor and the full supervised PC predictor. It also lists the raw score- for survival data, this is the Cox score for that feature; for regression, it is the standardized regression coefficient. If fitred.cv is supplied, the function also reports the average rank of the gene in the cross-validation folds, and the proportion of times that the gene is chosen (at the given threshold) in the cross-validation folds.

Author(s)

• "Eric Bair, Ph.D."

• "Jean-Eudes Dazard, Ph.D."

• "Rob Tibshirani, Ph.D."

Maintainer: "Jean-Eudes Dazard, Ph.D."

References

• E. Bair and R. Tibshirani (2004). "Semi-supervised methods to predict patient survival from gene expression data." PLoS Biol, 2(4):e108.

• E. Bair, T. Hastie, D. Paul, and R. Tibshirani (2006). "Prediction by supervised principal components." J. Am. Stat. Assoc., 101(473):119-137.

Examples

set.seed(332)

#generate some data
x <- matrix(rnorm(50*30), ncol=30)
y <- 10 + svd(x[1:50,])$v[,1] + .1*rnorm(30)
ytest <- 10 + svd(x[1:50,])$v[,1] + .1*rnorm(30)
censoring.status <- sample(c(rep(1,20), rep(0,10)))
censoring.status.test <- sample(c(rep(1,20), rep(0,10)))

featurenames <- paste("feature", as.character(1:50), sep="")
data <- list(x=x, 
             y=y, 
             censoring.status=censoring.status, 
             featurenames=featurenames)
data.test <- list(x=x, 
                  y=ytest, 
                  censoring.status=censoring.status.test, 
                  featurenames=featurenames)

a <- superpc.train(data, type="survival")
fit.red <- superpc.predict.red(a, 
                               data, 
                               data.test, 
                               .6)
superpc.listfeatures(data, 
                     a,  
                     fit.red, 
                     num.features=10)

superpc documentation built on Oct. 24, 2020, 1:07 a.m.