extract.pars {FTICRMS}R Documentation

Extract Parameters from File

Description

Extracts the parameters in the file specified by par.file and returns them in list form.

Usage

extract.pars(par.file = "parameters.RData", root.dir = ".")

Arguments

root.dir string containing location of parameters file to be extracted from
par.file string containing name of parameters file

Details

Used by run.analysis to record all the parameter choices in an analysis for future reference.

Value

A list with the following components:

add.norm logical; whether to normalize additively or multiplicatively on the log scale
add.par additive parameter for "shiftedlog" or "glog" options for trans.method
align.method alignment algorithm for peaks
base.dir directory for baseline-corrected files
clust.constant parameter used in running cluster.method
clust.method method for determining when two peaks from different spectra are the same
cor.thresh threshhold correlation for declaring isotopes
covariates data frame containing covariates used in analysis
FDR False Discovery Rate in Benjamini-Hochberg test
form formula used in t.test or lm
frac.changed convergence criterion in baseline calculation
isotope.dist maximum distance for declaring isotopes
k.biweight parameter for robust center and scale estimation using Tukey's biweight
lrg.dir directory for significant peaks file
lrg.only whether to consider only peaks that have at least one peak “large”; i.e., identified by run.lrg.peaks
masses specific masses to test
max.iter convergence criterion in baseline calculation
neg.pen negativity penalty in baseline calculation
normalization type of normalization to use on spectra before statistical analysis
num.pts number of points needed for peak fitting
oneside.min minimum number of points on each side of local maximum for peak fitting
overwrite whether to replace existing files with new ones
peak.dir directory for peak location files
peak.method method for locating peaks
pval.fcn function to calculate p-values if use.t.test = FALSE
R2.thresh R^2 value needed for peak fitting
raw.dir directory for raw data files
repl.method how to deal with replicates
res.dir directory for result file
root.dir directory for parameters file and raw data directory
sm.par smoothing parameter for baseline calculation
trans.method data transformation method
use.t.test whether to use a t-test to calculate p-values

Note

do.call(make.par.file, extract.pars()) recreates the original parameter file

Author(s)

Don Barkauskas (barkda@wald.ucdavis.edu)

References

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.

See Also

make.par.file, run.analysis


[Package FTICRMS version 0.6 Index]