extract.pars {FTICRMS} | R Documentation |
Extracts the parameters in the file specified by par.file
and returns them in list form.
extract.pars(par.file = "parameters.RData", root.dir = ".")
par.file |
string containing name of parameters file |
root.dir |
string containing location of parameters file to be extracted from |
Used by run.analysis
to record all the parameter choices in an analysis for future reference.
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 |
calc.all.peaks |
whether to calculate all possible peaks or only sufficiently large ones |
cluster.constant |
parameter used in running cluster.method |
cluster.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 |
gengamma.quantiles |
whether to use generalized gamma quantiles when calculating large peaks |
halve.search |
whether to use a halving-line search if step leads to smaller value of function |
isotope.dist |
maximum distance for declaring isotopes |
lrg.dir |
directory for significant peaks file |
lrg.file |
name of file for storing large peaks |
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.div |
negativity divisor in baseline calculation |
neg.norm.by |
method for negativity penalty in baseline analysis |
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 |
par.file |
string containing name of parameters file |
peak.dir |
directory for peak location files |
peak.method |
method for locating peaks |
peak.thresh |
threshold for declaring large peak |
pre.align |
shifts to apply before running run.strong.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 |
rel.conv.crit |
whether convergence criterion should be relatiev to current baseline estimate |
repl.method |
how to deal with replicates |
res.dir |
directory for result file |
res.file |
name for results file |
root.dir |
directory for parameters file and raw data directory |
sm.div |
smoothness divisor in baseline calculation |
sm.norm.by |
method for smoothness penalty in baseline analysis |
sm.ord |
order of derivative to kill in baseline analysis |
sm.par |
smoothing parameter for baseline calculation |
subtract.base |
whether to subtract calculated baseline from spectrum |
tol |
convergence criterion in baseline calculation |
trans.method |
data transformation method |
use.t.test |
whether to use a t-test to calculate p-values |
zero.rm |
whether to replace zeros in spectra with average of surrounding values |
do.call(make.par.file, extract.pars())
recreates the original parameter file
Don Barkauskas (barkda@wald.ucdavis.edu)
Barkauskas, D.A. (2009) “Statistical Analysis of Matrix-Assisted Laser Desorption/Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Data with Applications to Cancer Biomarker Detection”. Ph.D. dissertation, University of California at Davis.
Barkauskas, D.A. et al. (2009) “Detecting glycan cancer biomarkers in serum samples using MALDI FT-ICR mass spectrometry data”. Bioinformatics, 25:2, 251–257.
Xi, Y. and Rocke, D.M. (2008) “Baseline Correction for NMR Spectroscopic Metabolomics Data Analysis”. BMC Bioinformatics, 9:324.