pamr.fdr

0th

Percentile

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

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

Details

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

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

Aliases
  • pamr.fdr
Examples
# NOT RUN {
suppressWarnings(RNGversion("3.5.0"))
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)
# }
Documentation reproduced from package pamr, version 1.56.1, License: GPL-2

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