pamr (version 1.25)

pamr.listgenes: 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.

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)