ppc.fdr {ppc}R Documentation

Function to estimate False Discovery rates for peaks in PPC analysis

Description

Estimate False Discovery rates for peaks in FDR analysis, using permutations of the sample labels

Usage

ppc.fdr(data, centroid.fit, peak.fit, split.fit, ppc.fit, user.parms)

Arguments

data List containing mass spec data
centroid.fit Result of call to ppc.make.centroid.list
peak.fit Result of call to ppc.predict.peaks
split.fit Result of call to ppc.find.splits
ppc.fit Result of call to ppc.predict
user.parms List of user defined parameters

Value

results Matrix with columns- threshold used, number of peaks found, FDR
pi0 Esimate of proportion of truly null peaks
threshold Vector of thresholds used

Author(s)

Balasubramanian Narasimhan and Rob Tibshirani

Examples

## for a complete worked example of this function in a PPC analysis  see
##  http://www-stat.stanford.edu/~tibs/PPC/Rdist/Rscript.rawdata

[Package ppc version 1.01 Index]