run.all {FTICRMS} | R Documentation |
A wrapper that calls all six functions needed for a full analysis.
run.all(root.dir = ".", par.file = "parameters.RData")
root.dir |
string containing location of raw data directory and parameters file |
par.file |
string containing the name of the 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Xi, Y. and Rocke, D.M. (2006) “Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis”, unpublished.
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, no. 1, 289–300.
make.par.file
, run.baselines
, run.peaks
,
run.lrg.peaks
, run.strong.peaks
, run.cluster.matrix
,
run.analysis