run.lrg.peaks {FTICRMS}R Documentation

Extract "Large" Peaks from Files

Description

Takes the files output by run.peaks, extracts “large” peaks, combines them into a single data frame, and writes the data frame to a file.

Usage

run.lrg.peaks(k.biweight = 6, trans.method = "shiftedlog", add.par = 10, 
              root.dir = ".", peak.dir, base.dir, lrg.dir, 
              lrg.file = "lrg.peaks.RData", overwrite = FALSE, 
              use.par.file = FALSE, par.file = "parameters.RData", 
              calc.all.peaks = TRUE)

Arguments

k.biweight parameter for robust center and scale estimation using Tukey's biweight
trans.method type of transformation to use on spectra before statistical analysis; currently, only "shiftedlog", "glog", and "none" are supported
add.par additive parameter for "shiftedlog" or "glog" options for trans.method
root.dir string containing location of raw data directory
peak.dir directory for peak location files; default is paste(root.dir, "/All_Peaks", sep = "")
base.dir directory for baseline-corrected files; default is paste(root.dir, "/Baseline_Corrected", sep = "")
lrg.dir directory for significant peaks file; default is paste(root.dir, "/Large_Peaks", sep = "")
lrg.file string containing name for significant peaks file
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
calc.all.peaks logical; whether all peaks were calculated when run.peaks was run

Details

Reads in information from each file created by run.peaks, extracts peaks which have zero weight in the spectrum they come from when using Tukey's biweight with parameter k.biweight to estimate center and scale, and creates the file lrg.file in lrg.dir. The resulting file contains the data frame lrg.peaks, which has columns
Center_hat estimated mass of peak
Max_hat estimated intensity of peak
Width_hat estimated width of peak
File name of file the peak was extracted from, with “_peaks.RData” deleted

and is ready to be used by run.strong.peaks.

Value

No value returned; the file is simply created.

Note

A peak is “large” if has zero weight in the data generated by run.peaks for the spectrum it comes from when using Tukey's biweight with parameter k.biweight to estimate center and scale.

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

See Also

run.peaks, run.cluster.matrix


[Package FTICRMS version 0.6 Index]