run.baselines {FTICRMS}R Documentation

Calculate Baselines for FT-ICR spectra

Description

Takes the spectra from files in raw.dir, calculates the baselines from them, and writes the results in the directory base.dir.

Usage

run.baselines(root.dir = ".", raw.dir, base.dir, overwrite = FALSE,
              use.par.file = FALSE, par.file = "parameters.RData",
              sm.par = 1e-11, sm.ord = 2, max.iter = 40, tol = 5e-8,
              sm.div = NA, sm.norm.by = c("baseline", "overestimate", "constant"),
              neg.div = NA, neg.norm.by = c("baseline", "overestimate", "constant"),
              rel.conv.crit = TRUE, zero.rm = TRUE, halve.search = FALSE)

Arguments

root.dir directory for parameters file and raw data
raw.dir directory for raw data files; default is paste(root.dir, "/Raw_Data", sep = "")
base.dir directory for baseline files; default is paste(root.dir, "/Baselines", sep = "")
overwrite whether to replace exisiting files with new ones
use.par.file logical; if TRUE, then parameters are read from par.file in directory root.dir
par.file string containing name of parameters file
sm.par smoothing parameter for baseline calculation
sm.ord order of derivative to kill in baseline analysis
max.iter convergence criterion in baseline calculation
tol convergence criterion; see below
sm.div smoothness divisor in baseline calculation
sm.norm.by method for smoothness penalty in baseline analysis
neg.div negativity divisor in baseline calculation
neg.norm.by method for negativity penalty in baseline analysis
rel.conv.crit logical; whether convergence criterion should be relatiev to current baseline estimate
zero.rm logical; whether to replace zeros with average of surrounding values
halve.search logical; whether to use a halving-line search if step leads to smaller value of function

Details

Goes through the entire directory raw.dir file-by-file and computes each baseline using baseline, then writes the spectrum and the baseline to a file in directory base.dir. The name of the new file is the same as the name of the old file with “.txt” replaced by “.RData”, and the new file is ready to be used by run.peaks.

See baseline for descriptions of all the parameters after par.file.

Value

No value returned; the files are simply created.

Note

If use.par.file = TRUE, then the parameters read in from the file overwrite any arguments entered in the function call.

Author(s)

Don Barkauskas (barkda@wald.ucdavis.edu)

References

Barkauskas, D.A. (2009) “Statistical Analysis of Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Data with Applications to Cancer Biomarker Detection”. Ph.D. dissertation, University of California at Davis.

Barkauskas, D.A. et al. (2009) “Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data”. Bioinformatics, 25:2, 251–257.

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

See Also

baseline, run.peaks


[Package FTICRMS version 0.7 Index]