pamr (version 1.57)

pamr.plotcvprob: A function to plot the cross-validated sample probabilities from the nearest shrunken centroid classifier

Description

A function to plot the cross-validated sample probabilities from the nearest shrunken centroid classifier

Usage

pamr.plotcvprob(fit, data, threshold)

Arguments

fit

The result of a call to pamr.cv

data

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

Threshold value to be used

Author

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

Details

pamr.plotcvprob plots the cross-validated sample probabilities the from nearest shrunken centroid classifier, stratified by the true classses.

Examples

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)