ppc.read.raw.nobatch {ppc}R Documentation

A function to read in raw protein mass spec data, with no batches

Description

This function reads in raw protein mass spec data from a directory. The directory is assumed to have on subdirectory per class (eg control or disease). There is one comma-separated (csv) file in the subdirectory per spectrum, having lines of the form m/ value, intensity (one line per m/z site)

Usage

ppc.read.raw.nobatch(directory, mz = NULL)

Arguments

directory Name of directory containing the data
mz Optional vector of m/z values. Default NULL. If NULL, m/z values are read in from files. Otherwise the values in mz are used.

Value

xtr Matrix of intensities- one row per m/z site, one col per spectrum
mz m/z values
filenames List of names of files that were read in

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]