R: A function to list the genes that survive the thresholding,...

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, fitcv=NULL, 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
`fitcv` | Optional object, result of a call to pamr.cv
`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. If fitcv is provided, the function also reports the average rank of the gene in the cross-validation folds, and the proportion of times that the gene is chosen (at the given threshold) in the cross-validation folds.

### Author(s)

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

### 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 1.55 Index]