run.peaks {FTICRMS} | R Documentation |
Takes baseline-corrected data and locates potential peaks in the spectra.
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)
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 |
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
.
No value returned; the files are simply created.
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.
Don Barkauskas (barkda@wald.ucdavis.edu)
Barkauskas, D.A. et al. (2008) “Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data”. Submitted to Bioinformatics
run.baselines
, run.lrg.peaks
, locate.peaks