run.lrg.peaks {FTICRMS} | R Documentation |
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.
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)
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 |
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
.
No value returned; the file is simply created.
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.
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