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(numsds = 4, 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)
numsds |
number of standard deviations above the mean to be declared non-noise |
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 are
numsds
standard deviations above the mean value in the spectrum they come from, 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 its value of Max_hat
is at least numsds
standard
deviations above the mean value in the data generated by run.peaks
for the
spectrum it comes from.
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