run.lrg.peaks: 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(trans.method = c("shiftedlog", "glog", "none"),  add.par = 0, subtract.base = FALSE, 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 = FALSE, gengamma.quantiles = TRUE, peak.thresh = 3.798194, subs)

Arguments

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

peak.dir

directory for peak location files; default is paste(root.dir, "/All_Peaks", sep = "")

base.dir

directory for baseline files; default is paste(root.dir, "/Baselines", sep = "")

lrg.dir

directory for large peaks file; default is paste(root.dir, "/Large_Peaks", sep = "")

lrg.file

name of file to store large peaks in

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 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

subs

subset of spectra to use for analysis; see below

Value

No value returned; the file is simply created.

Details

Reads in information from each file created by run.peaks, extracts peaks which are “large” (see below), 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.

References

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.