A function to plot the cross-validated sample probabilities from the nearest shrunken centroid classifier
pamr.plotcvprob(fit, data, threshold)The result of a call to pamr.cv
A list with at least two components: x- an expression genes in the rows, samples in the columns), and y- a vector of the class labels for each sample. Same form as data object used by pamr.train.
Threshold value to be used
Trevor Hastie,Robert Tibshirani, Balasubramanian Narasimhan, and Gilbert Chu
pamr.plotcvprob plots the cross-validated sample probabilities the
from nearest shrunken centroid classifier, stratified by the true classses.
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.plotcvprob(mycv,mydata,threshold=1.6)
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