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=F)

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

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,geneid=as.character(1:1000))
mytrain <-   pamr.train(mydata)
mycv <- pamr.cv(mytrain,mydata)
pamr.listgenes(mytrain, mydata, threshold=1.6)
 

[Package pamr version 1.12.1 Index]