run.all: Complete Analysis of FT-ICR MS Data

In FTICRMS: Programs for Analyzing Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry 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.

Note

The analysis described in Barkauskas et al. (2008) can be (approximately) reproduced using the following parameter values instead of the defaults:

add.par = 10

calc.all.peaks = TRUE

gengamma.quantiles = FALSE

max.iter = 30

neg.norm.by = "constant"

peak.thresh = 4

pval.fcn = function(x){anova(x)[2,5]}

rel.conv.crit = FALSE

sm.norm.by = "constant"

subtract.base = TRUE

zero.rm = FALSE

(It is only an approximate reproduction because the stopping criterion for baseline calculation used in the article turned out to be a poor one and is no longer supported in the package. This shouldn't make a very large difference, however.)

Author(s)

Don Barkauskas ([e-mail])

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

FTICRMS documentation built on May 1, 2019, 10:53 p.m.