pamr.geneplot {pamr}

A function to plot the genes that surive the thresholding from the nearest shrunken centroid classifier

Description

A function to plot the genes that survive the thresholding, from the nearest shrunken centroid classifier produced by pamr.train

Usage

pamr.geneplot(fit, data, threshold)

Arguments

fit

The result of a call to pamr.train

data

The input data. In the same format as the input data for pamr.train

threshold

The desired threshold value

Details

pamr.geneplot Plots the raw gene expression for genes that survive the specified threshold. Plot is stratified by class. Plot is set up to display only up to about 20 or 25 genes, otherwise it gets too crowded. Hence threshold should be chosen to yield at most about 20 or 25 genes.

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)
pamr.geneplot(mytrain, mydata, threshold=1.6)