pamr.listgenes {pamr} | R Documentation

## A function to list the genes that survive the thresholding, from the nearest shrunken centroid classifier

### Description

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

### Usage

    pamr.listgenes(fit, data,  threshold, genenames=FALSE)

### 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
`genenames` | Include genenames in the list? If yes, they are taken from "data". Default is false (geneid is always included in the list).

### Details

`pamr.listgenes` List the geneids, and standardized centroids for each class, for genes surviving at the given threshold.

### Author(s)

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

### References

### Examples

    #generate some data
    set.seed(120)
    x <- matrix(rnorm(1000*20),ncol=20)
    y <- sample(c(1:4),size=20,replace=TRUE)

    mydata <- list(x=x,y=factor(y), geneid=as.character(1:nrow(x)), genenames=paste("g",as.character(1:nrow(x)),sep=""),)

    #train classifier
    mytrain<-   pamr.train(mydata)

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

[Package pamr version 1.22 Index]