ppc.predict1 {ppc}R Documentation

Function to do a single test set prediction for the PPC method

Description

This function does test set prediction for PPC method. It predicts outcome classes for a list of peaks from a single test set spectrum.

Usage

ppc.predict1(centroid.fit, split.fit, logmz, peaklist.te,  threshold, metric = c("binomial", "euclidean", "absolute"), summ = c("mean", "median"))

Arguments

centroid.fit Result of a call to ppc.make.centroid.list
split.fit Result of a call to ppc.find.splits
logmz log of m/z values from training data
peaklist.te List of peaks from test set- each component is a matrix of log m/z values and peak intensities
threshold Threshold values to use
metric "binomial","euclidean", or "absolute"
summ "mean" or median"

Value

yhat Matrix of predicted classes
threshold Threshold values used.
numsites Number of sites surviving the threshold for each shrinkage value
sites List of sites surviving the threshold for each shrinkage value
ind Indicator matrix of event ( peak intensity at site > cutpoint
ind0 Indicator matrix of event ( peak intensity at site > cutpoint
prob Matrix of estimated class probabilities
ht Matrix of peak intensities

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]