TargetSearch: A package for the analysis of GC-MS metabolite profiling data

This packages provides a targeted pre-processing method for GC-MS data.

Author
Alvaro Cuadros-Inostroza <inostroza@mpimp-golm.mpg.de>, Jan Lisec <lisec@mpimp-golm.mpg.de>, Henning Redestig <henning.red@googlemail.com>, Matt Hannah <matthew.hannah@bayercropscience.com>
Date of publication
None
Maintainer
Alvaro Cuadros-Inostroza <inostroza@mpimp-golm.mpg.de>
License
GPL (>= 2)
Version
1.30.0

View on Bioconductor

Man pages

baseline
Baseline correction algorithm
defunct
Defunct functions in package 'TargetSearch'
FAMEoutliers
FAME outlier detection
file
Convert RI files from text to binary format and viceversa.
FindPeaks
Extract peaks from chromatogram files
fixRI
Fixing Retention Time Index Correction
ImportFameSettings
Retention time markers settings
ImportLibrary
Library import
ImportSamples
Sample definitions
medianRILib
Median RI library correction
NetCDFPeakFinding
Peak picking algorithm from CDF files
peakCDFextraction
NetCDF to R
peakFind
Intensities and RI matrices
plotFAME
Plot a standard marker
plotPeak
Plot peaks
plotPeakSimple
Plot peaks - simple interface
plotRIdev
Plot Retention Time Index Deviation
plotSpectra
Plot a Spectra Comparison
Profile
Average the correlating masses for each metabolite
ProfileCleanUp
Reduce redundancy of the profile
quantMatrix
Create an intensity matrix using quantification masses
ri2rt
Retention Time Index to Retention Time convertion
RIcorrect
Peak picking from CDF files and RI correction
riMatrix
Retention Time Index Matrix
rt2ri
Retention Time to Retention Time Index convertion
sampleRI
Sample especific RI detection
TargetSearchGUI
A GUI for TargetSearch
TargetSearch-package
A targeted approach for GC-MS data.
tsLib-class
Class for representing a reference library
tsMSdata-class
Class for representing MS data
tsProfile-class
Class for representing a MS profile
tsRim-class
Class for representing retention index markers
tsSample-class
Class for representing samples
writeLibText
Save a library object in text format
writeMSP
Save spectra in MSP format to be visualized in NIST
Write.Results
Save TargetSearch result objects into files

Files in this package

TargetSearch/.BBSoptions
TargetSearch/DESCRIPTION
TargetSearch/NAMESPACE
TargetSearch/R
TargetSearch/R/FAMEoutliers.R
TargetSearch/R/FindPeaks.R
TargetSearch/R/ImportFameSettings.R
TargetSearch/R/ImportLibrary.R
TargetSearch/R/ImportSamples.R
TargetSearch/R/NetCDFPeakFinding.R
TargetSearch/R/Profile.R
TargetSearch/R/ProfileCleanUp.R
TargetSearch/R/ProgressBar.R
TargetSearch/R/RIcorrect.R
TargetSearch/R/TargetSearchGUI.R
TargetSearch/R/Write.Results.R
TargetSearch/R/baseline.R
TargetSearch/R/classes.R
TargetSearch/R/dayNorm.R
TargetSearch/R/file.R
TargetSearch/R/findRetentionTime.R
TargetSearch/R/fixRI.R
TargetSearch/R/medianRILib.R
TargetSearch/R/methods-tsLib.R
TargetSearch/R/methods-tsProfile.R
TargetSearch/R/methods-tsRim.R
TargetSearch/R/methods-tsSample.R
TargetSearch/R/netCDF.R
TargetSearch/R/peakCDFextraction.R
TargetSearch/R/peakFind.R
TargetSearch/R/plot.R
TargetSearch/R/plotFAME.R
TargetSearch/R/quantMatrix.R
TargetSearch/R/rt2ri.R
TargetSearch/R/sampleRI.R
TargetSearch/R/writeLibText.R
TargetSearch/R/writeRIFile.R
TargetSearch/build
TargetSearch/build/vignette.rds
TargetSearch/inst
TargetSearch/inst/CITATION
TargetSearch/inst/NEWS
TargetSearch/inst/doc
TargetSearch/inst/doc/RICorrection.R
TargetSearch/inst/doc/RICorrection.Rnw
TargetSearch/inst/doc/RICorrection.pdf
TargetSearch/inst/doc/TargetSearch.R
TargetSearch/inst/doc/TargetSearch.Rnw
TargetSearch/inst/doc/TargetSearch.pdf
TargetSearch/inst/ico
TargetSearch/inst/ico/Icon_TSGUI.ico
TargetSearch/man
TargetSearch/man/FAMEoutliers.Rd
TargetSearch/man/FindPeaks.Rd
TargetSearch/man/ImportFameSettings.Rd
TargetSearch/man/ImportLibrary.Rd
TargetSearch/man/ImportSamples.Rd
TargetSearch/man/NetCDFPeakFinding.Rd
TargetSearch/man/Profile.Rd
TargetSearch/man/ProfileCleanUp.Rd
TargetSearch/man/RIcorrect.Rd
TargetSearch/man/TargetSearch-package.Rd
TargetSearch/man/TargetSearchGUI.Rd
TargetSearch/man/Write.Results.Rd
TargetSearch/man/baseline.Rd
TargetSearch/man/defunct.Rd
TargetSearch/man/file.Rd
TargetSearch/man/fixRI.Rd
TargetSearch/man/medianRILib.Rd
TargetSearch/man/peakCDFextraction.Rd
TargetSearch/man/peakFind.Rd
TargetSearch/man/plotFAME.Rd
TargetSearch/man/plotPeak.Rd
TargetSearch/man/plotPeakSimple.Rd
TargetSearch/man/plotRIdev.Rd
TargetSearch/man/plotSpectra.Rd
TargetSearch/man/quantMatrix.Rd
TargetSearch/man/ri2rt.Rd
TargetSearch/man/riMatrix.Rd
TargetSearch/man/rt2ri.Rd
TargetSearch/man/sampleRI.Rd
TargetSearch/man/tsLib-class.Rd
TargetSearch/man/tsMSdata-class.Rd
TargetSearch/man/tsProfile-class.Rd
TargetSearch/man/tsRim-class.Rd
TargetSearch/man/tsSample-class.Rd
TargetSearch/man/writeLibText.Rd
TargetSearch/man/writeMSP.Rd
TargetSearch/src
TargetSearch/src/Rinit.c
TargetSearch/src/file.c
TargetSearch/src/file.h
TargetSearch/src/find_peaks.c
TargetSearch/src/find_peaks.h
TargetSearch/src/getLine.c
TargetSearch/src/getLine.h
TargetSearch/src/hpf.c
TargetSearch/src/ncdf.c
TargetSearch/src/netcdf_peak_finding.c
TargetSearch/src/peakExtraction.c
TargetSearch/src/ppc.c
TargetSearch/vignettes
TargetSearch/vignettes/RICorrection.Rnw
TargetSearch/vignettes/RetentionIndexCorrection.R
TargetSearch/vignettes/TargetSearch.Rnw
TargetSearch/vignettes/biblio.bib
TargetSearch/vignettes/tsGUI.png