make.par.file {FTICRMS}R Documentation

Create Parameter File for FT-ICR MS Analysis

Description

Creates a file of parameters that can be read by the functions in the FTICRMS package

Usage

make.par.file(covariates, form, par.file = "parameters.RData", root.dir = ".", ...)

Arguments

covariates data frame with rownames given by raw data files
form object of class “formula” to be used for testing using covariates
par.file string containing name of file
root.dir string containing location for file
... parameters whose default values are to be overwritten (see below)

Details

Creates a file with name given by par.file in directory given by root.dir which contains values for all of the parameters used in the programs in the FTICRMS package. The possible parameters that can be included in ..., their default values, their descriptions, and the program(s) in which they are used are as follows:
add.norm = TRUE logical; whether to normalize additively or multiplicatively on the log scale run.analysis
add.par = 0 additive parameter for "shiftedlog" or "glog" options for trans.method run.cluster.matrix, run.lrg.peaks, run.peaks
align.method = "spline" alignment algorithm for peaks run.cluster.matrix
base.dir = paste(root.dir, "/Baselines", sep = "") directory for baseline files run.baselines, run.cluster.matrix, run.lrg.peaks, run.peaks
calc.all.peaks = FALSE logical; whether to calculate all possible peaks or only sufficiently large ones run.cluster.matrix, run.lrg.peaks, run.peaks
cluster.constant = 10 NA run.cluster.matrix
cluster.method = "ppm" NA run.cluster.matrix
cor.thresh = 0.8 threshold correlation for declaring isotopes run.strong.peaks
FDR = 0.1 False Discovery Rate in Benjamini-Hochberg test run.analysis
gengamma.quantiles = TRUE logical; whether to use generalized gamma quantiles when calculating large peaks run.lrg.peaks, run.peaks
halve.search = FALSE logical; whether to use a halving-line search if step leads to smaller value of function run.baselines
isotope.dist = 7 maximum distance for declaring isotopes run.analysis, run.cluster.matrix, run.strong.peaks
lrg.dir = paste(root.dir, "/Large_Peaks", sep = "") directory for large peaks file run.analysis, run.cluster.matrix, run.lrg.peaks, run.strong.peaks
lrg.file = "lrg_peaks.RData" name of file for storing large peaks run.analysis, run.cluster.matrix, run.lrg.peaks, run.strong.peaks
lrg.only = TRUE logical; whether to consider only peaks that have at least one “large”peak; i.e., identified by run.lrg.peaks run.analysis, run.cluster.matrix
masses = NULL specific masses to test run.analysis, run.cluster.matrix
max.iter = 40 convergence criterion in baseline calculation run.baselines
neg.div = NA negativity divisor in baseline calculation run.baselines
neg.norm.by = c("baseline", "overestimate", "constant") method for negativity penalty in baseline analysis run.baselines
normalization = "common" type of normalization to use on spectra before statistical anlaysis run.analysis
num.pts = 5 number of consecutive points needed for peak fitting run.cluster.matrix, run.peaks
oneside.min = 1 minimum number of points on each side of local maximum for peak fitting run.cluster.matrix, run.peaks
overwrite = FALSE whether to replace exisiting files with new ones All six programs
par.file = "parameters.RData" string containing name of parameters file All six programs
peak.dir = paste(root.dir, "/All_Peaks", sep = "") directory for peak location files run.cluster.matrix, run.lrg.peaks, run.peaks
peak.method = "parabola" method for locating peaks run.cluster.matrix, run.peaks
peak.thresh = 3.798194 threshold for declaring large peak run.lrg.peaks, run.peaks
pre.align = FALSE shifts to apply before running run.strong.peaks run.cluster.matrix, run.strong.peaks
pval.fcn = "default" function to calculate p-values if use.t.test = FALSE run.analysis
R2.thresh = 0.98 R^2 value needed for peak fitting run.cluster.matrix, run.peaks
raw.dir = paste(root.dir, "/Raw_Data", sep = "") directory for raw data files run.baselines
rel.conv.crit = TRUE whether convergence criterion should be relatiev to current baseline estimate run.baselines
repl.method = max how to deal with replicates run.analysis
res.dir = paste(root.dir, "/Results", sep = "") directory for result file run.analysis
res.file = "analyzed.RData" name for results file run.analysis
root.dir = "." directory for parameters file and raw data All six programs
sm.div = NA smoothness divisor in baseline calculation run.baselines
sm.norm.by = c("baseline", "overestimate", "constant") method for smoothness penalty in baseline analysis run.baselines
sm.ord = 2 order of derivative to kill in baseline analysis run.baselines
sm.par = 1e-11 smoothing parameter for baseline calculation run.baselines
subtract.base = FALSE logical; whether to subtract calculated baseline from spectrum run.cluster.matrix, run.lrg.peaks, run.peaks
tol = 5e-8 convergence criterion in baseline calculation run.baselines
trans.method = "shiftedlog" data transformation method run.cluster.matrix, run.lrg.peaks, run.peaks
use.t.test = FALSE whether to use a t-test to calculate p-values run.analysis
zero.rm = TRUE whether to replace zeros in spectra with average of surrounding values run.baselines

Value

No value returned; the file par.file is simply created in root.dir.

Note

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

See the individual function help pages for each function for more detailed descriptions of the above parameters.

Author(s)

Don Barkauskas (barkda@wald.ucdavis.edu)

References

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 Bioiniformatics, 9:324.

See Also

extract.pars


[Package FTICRMS version 0.7 Index]