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

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 1.28.0 Index]