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

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

AuthorAlvaro 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 publicationNone
MaintainerAlvaro Cuadros-Inostroza <inostroza@mpimp-golm.mpg.de>
LicenseGPL (>= 2)
Version1.30.0

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

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