run.all {FTICRMS}R Documentation

Complete Analysis of FT-ICR MS Data

Description

A wrapper that calls all six functions needed for a full analysis.

Usage

run.all(par.file = "parameters.RData", root.dir = ".")

Arguments

par.file string containing the name of the parameters file
root.dir string containing location of raw data directory and parameters file

Details

Requires par.file to be in place before starting—for example by creating it with make.par.file.

Calls (in order) run.baselines, run.peaks, run.lrg.peaks, run.strong.peaks, run.cluster.matrix, and run.analysis.

Author(s)

Don Barkauskas (barkda@wald.ucdavis.edu)

References

Barkauskas, D.A. et al. (2008) “Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data”. Submitted to Bioinformatics

Xi, Y. and Rocke, D.M. (2008) “Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis”. BMC Bioinformatics, 9:324.

Benjamini, Y. and Hochberg, Y. (1995) “Controlling the false discovery rate: a practical and powerful approach to multiple testing.” J. Roy. Statist. Soc. Ser. B, 57:1, 289–300.

See Also

make.par.file, run.baselines, run.peaks, run.lrg.peaks, run.strong.peaks, run.cluster.matrix, run.analysis


[Package FTICRMS version 0.6 Index]