A function giving prediction information, from a nearest shrunken centroid fit.

Description

A function giving prediction information, from a nearest shrunken centroid fit

Usage

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pamr.predict(fit, newx, threshold,
             type = c("class", "posterior", "centroid", "nonzero"),
             prior = fit$prior, threshold.scale = fit$threshold.scale)

Arguments

fit

The result of a call to pamr.train

newx

Matrix of features at which predictions are to be made

threshold

The desired threshold value

type

Type of prediction desired: class predictions, posterior probabilities, (unshrunken) class centroids, vector of genes surviving the threshold

prior

Prior probabilities for each class. Default is that specified in "fit"

threshold.scale

Additional scaling factors to be applied to the thresholds. Vector of length equal to the number of classes. Default is that specified in "fit".

Details

pamr.predict Give a cross-tabulation of true versus predicted classes for the fit returned by pamr.train or pamr.cv, at the specified threshold

Author(s)

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

Examples

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set.seed(120)
x <- matrix(rnorm(1000*20),ncol=20)
y <- sample(c(1:4),size=20,replace=TRUE)
mydata <- list(x=x,y=y)
mytrain <-   pamr.train(mydata)
mycv <- pamr.cv(mytrain,mydata)
pamr.predict(mytrain, mydata$x , threshold=1)
 

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