pamr.predict: A function giving prediction information, from a nearest...
In pamr: Pam: Prediction Analysis for Microarrays

Description Usage Arguments Details Author(s) Examples

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

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

`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".

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

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

suppressWarnings(RNGversion("3.5.0"))
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)

Loading required package: cluster
Loading required package: survival
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