run.baselines {FTICRMS}R Documentation

Create Baseline-Corrected Spectra for FT-ICR MS

Description

Takes the spectra from files in raw.dir, calculates and subtracts 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.fac = 10^15, neg.pen = sqrt(pi/2), max.iter = 30, 
              frac.changed = 0.001, binsize = 64)

Arguments

root.dir string containing location of raw data directory
raw.dir directory for raw data files; default is paste(root.dir, "/Raw_Data", sep = "")
base.dir directory for baseline-corrected files; default is paste(root.dir, "/Baseline_Corrected", 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.fac smoothing factor for baseline calculation
neg.pen negativity penalty in baseline calculation
max.iter convergence criterion in baseline calculation
frac.changed convergence criterion in baseline calculation
binsize size of bins used in estimating noise variance in baseline calculation

Details

Goes through the entire directory raw.dir file-by-file and computes each baseline using baseline, subtracts the baseline from the spectrum, and writes the resulting data frame 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.

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. 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Xi, Y. and Rocke, D.M. (2006) “Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis”, unpublished.

See Also

baseline, run.peaks

Examples






[Package FTICRMS version 0.5 Index]