pamr.plotcvprob: A function to plot the cross-validated sample probabilities...

In pamr: Pam: Prediction Analysis for Microarrays

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

Details

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

Author(s)

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

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)

pamr documentation built on July 1, 2024, 9:06 a.m.