run.all {FTICRMS} | R Documentation |
A wrapper that calls all six functions needed for a full analysis.
run.all(par.file = "parameters.RData", root.dir = ".")
par.file |
string containing the name of the parameters file |
root.dir |
string containing location of raw data directory and parameters file |
Requires par.file
to be in place before starting—for example by creating it with
make.par.file
.
Calls (in order) run.baselines
, run.peaks
, run.lrg.peaks
,
run.strong.peaks
, run.cluster.matrix
, and run.analysis
.
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
Xi, Y. and Rocke, D.M. (2008) “Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis”. BMC Bioinformatics, 9:324.
Benjamini, Y. and Hochberg, Y. (1995) “Controlling the false discovery rate: a practical and powerful approach to multiple testing.” J. Roy. Statist. Soc. Ser. B, 57:1, 289–300.
make.par.file
, run.baselines
, run.peaks
,
run.lrg.peaks
, run.strong.peaks
, run.cluster.matrix
,
run.analysis