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 = ".")
root.dir |
string containing location of parameters file to be extracted from |
par.file |
string containing name of parameters file |
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 |
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 |
do.call(make.par.file, extract.pars())
recreates the original parameter file
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.