run.peaks {FTICRMS}R Documentation

Locate Potential Peaks in FT-ICR MS Spectra

Description

Takes baseline-corrected data and locates potential peaks in the spectra.

Usage

run.peaks(add.par = 10, trans.method = "shiftedlog", root.dir = ".", 
          base.dir, peak.dir, overwrite = FALSE, use.par.file = FALSE, 
          par.file = "parameters.RData", num.pts = 5, R2.thresh = 0.98, 
          oneside.min = 1, peak.method = "parabola", 
          calc.all.peaks = TRUE, numsds = 4)

Arguments

add.par additive parameter for "shiftedlog" or "glog" options for trans.method
trans.method type of transformation to use on spectra before statistical analysis; currently, only "shiftedlog", "glog", and "none" are supported
root.dir string containing location of raw data directory
base.dir directory for baseline-corrected files; default is paste(root.dir, "/Baseline_Corrected", sep = "")
peak.dir directory for peak location files; default is paste(root.dir, "/All_Peaks", 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
num.pts minimum number of points needed to have a peak
R2.thresh minimum R^2 needed to have a peak
oneside.min minimum number of points needed on each side of the local maximum
peak.method method to use for locating peaks; currently only "parabola" and "locmax" are supported
calc.all.peaks logical; whether or not to locate all peaks or only those which are sufficiently large
numsds only relevant if calc.all.peaks = FALSE; the number of standard deviations above the mean required for a peak to be considered

Details

Reads in information from each file created by run.baselines, calls locate.peaks to find potential peaks, and writes the output to a file in directory peak.dir. The name of each new file is the same as the name of the old file with “.RData” replaced by “_peaks.RData”. The resulting file contains the data frame all.peaks, which has columns
Center_hat estimated mass of peak
Max_hat estimated intensity of peak
Width_hat estimated width of peak

and is ready to be used by run.lrg.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.

Using calc.all.peaks = FALSE will speed up computation time immensely, but will affect the final result. It probably won't affect it much, but caveat emptor.

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

See Also

run.baselines, run.lrg.peaks, locate.peaks


[Package FTICRMS version 0.6 Index]