FTICRMS (version 0.8)

run.all: 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.

References

Barkauskas, D.A. and D.M. Rocke. (2009a) A general-purpose baseline estimation algorithm for spectroscopic data. to appear in Analytica Chimica Acta. doi:10.1016/j.aca.2009.10.043 Barkauskas, D.A. et al. (2009b) Analysis of MALDI FT-ICR mass spectrometry data: A time series approach. Analytica Chimica Acta, 648:2, 207--214. Barkauskas, D.A. et al. (2009c) Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data. Bioinformatics, 25:2, 251--257. 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. Xi, Y. and Rocke, D.M. (2008) Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis. BMC Bioinformatics, 9:324.

See Also

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