pamr (version 1.54.1)

pamr.fdr: A function to estimate false discovery rates for the nearest shrunken centroid classifier

Description

A function to estimate false discovery rates for the nearest shrunken centroid classifier

Usage

pamr.fdr(trained.obj, data,  nperms=100, 
 xl.mode=c("regular","firsttime","onetime","lasttime"),xl.time=NULL, xl.prevfit=NULL)

Arguments

trained.obj

The result of a call to pamr.train

data

Data object; same as the one passed to pamr.train

nperms

Number of permutations for estimation of FDRs. Default is 100

xl.mode

Used by Excel interface

xl.time

Used by Excel interface

xl.prevfit

Used by Excel interface

Value

• A list with components:
• results
  Matrix of estimates FDRs for various various threshold values. Reported are both the median and 90th percentile of the FDR over permutations
• pi0
  The estimated proportion of genes that are null, i.e. not significantly different

Details

pamr.fdr estimates false discovery rates for a nearest shrunken centroid classifier

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=factor(y), geneid=as.character(1:nrow(x)),
               genenames=paste("g",as.character(1:nrow(x)),sep=""))

mytrain <-   pamr.train(mydata)
myfdr <- pamr.fdr(mytrain, mydata)