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

A function to read in raw protein mass spec data, with 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). The subdirectories like "control" have further subdirectories, one per batch. So the structure looks lik control/batch1/file.csv, control/batch2/file.csv, disease/batch1/file.csv, etc. There is one comma-separated (csv) file.csv in the subdirectory per spectrum, having lines of the form m/ value, intensity (one line per m/z site)

Usage

ppc.read.raw.batch(dir, batches, mz = NULL)

Arguments

dir Name of directory containing the data
batches Vector of character names of batches
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 filenames 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]