run.peaks: Locate Potential Peaks in FT-ICR MS Spectra
In FTICRMS: Programs for Analyzing Fourier Transform-Ion Cyclotron Resonance Mass Spectrometry Data

Description Usage Arguments Details Value Note Author(s) References See Also

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

run.peaks(trans.method = c("shiftedlog", "glog", "none"),
          add.par = 0, subtract.base = FALSE, 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 = c("parabola", "locmaxes"), 
          calc.all.peaks = FALSE, gengamma.quantiles = TRUE, 
          peak.thresh = 3.798194)

`trans.method`	type of transformation to use on spectra before statistical analysis
`add.par`	additive parameter for `"shiftedlog"` or `"glog"` options for `trans.method`
`subtract.base`	logical; whether to subtract calculated baseline from spectrum
`root.dir`	directory for parameters file and raw data
`base.dir`	directory for baseline files; default is `paste(root.dir, "/Baselines", 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`	number of consecutive points needed for peak fitting
`R2.thresh`	R^2 value needed for peak fitting
`oneside.min`	minimum number of points on each side of local maximum for peak fitting
`peak.method`	method for locating peaks
`calc.all.peaks`	logical; whether to calculate all possible peaks or only sufficiently large ones
`gengamma.quantiles`	logical; whether to use generalized gamma quantiles when calculating large peaks
`peak.thresh`	threshold for declaring large peak; see below

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.

The parameters gengamma.quantiles and peak.thresh are relevant only if calc.all.peaks = FALSE. In that case, if gengamma.quantiles == TRUE, then peak.thresh is interpreted as a multiplier for the baseline. Anything larger than peak.thresh times the estimated baseline is declared to be a real peak. If gengamma.quantiles == FALSE, then peak.thresh is interpreted as two-thirds of the value of K used in a Tukey's biweight estimation of center and scale (so roughly equal to the number of standard deviations above the mean for iid normal data). Anything with weight zero in the calculation is then declared to be a real peak.

No value returned; the files are simply created.

If use.par.file == TRUE and other parameters are entered into the function call, then the parameters entered in the function call overwrite those read in from the file. Note that this is opposite from the behavior for FTICRMS versions 0.7 and earlier.

peak.method and trans.method can be abbreviated.

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

Don Barkauskas (barkda@wald.ucdavis.edu)

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.

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

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