pamr.listgenes {pamr} | R Documentation |
A function to list the genes that survive the thresholding, from the nearest shrunken centroid classifier produced by pamr.train
pamr.listgenes(fit, data, threshold, genenames=F)
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). |
pamr.listgenes
List the geneids, and standardized centroids for
each class, for genes surviving at the given threshold.
Trevor Hastie, Robert Tibshirani, Balasubramanian Narasimhan, and Gilbert Chu
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)