run.baselines: Calculate and Store Baselines for Spectroscopic Data

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 = 20, 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

logical; whether to replace existing 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 penalize in baseline analysis

max.iter

convergence criterion in baseline calculation

tol

convergence criterion

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 relative to size of 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

Value

No value returned; the files are simply created.

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.

The files in raw.dir must be in a specific format (future versions of the package will allow for more flexibility). The files should be two-column text files with mass in the first column and spectrum intensity in the second column. There should be no header row (just start the file with the first data point). The columns can be either comma-separated or whitespace-separated and the program will automatically detect which each file is. The decimal separator should be ".", as using "," will cause errrors in reading the files.

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

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.