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

Functions

as.list.tsMSdata Man page
as.list,tsMSdata-method Man page
as.list.tsMSdata,tsMSdata-method Man page
as.list.tsProfile Man page
as.list.tsProfile,tsMSdata-method Man page
baseline Man page
baselineCorrection Man page
bin2text Man page
CDFfiles Man page
CDFfiles<- Man page
CDFfiles<-,tsSample-method Man page
CDFfiles,tsSample-method Man page
CDFpath Man page
CDFpath<- Man page
CDFpath<-,tsSample-method Man page
CDFpath,tsSample-method Man page
FAMEoutliers Man page
fileFormat Man page
fileFormat<- Man page
fileFormat<-,tsSample-method Man page
fileFormat,tsSample-method Man page
FindPeaks Man page
fixRI Man page
fixRIcorrection Man page
fixRIcorrection-defunct Man page
ImportFameSettings Man page
ImportLibrary Man page
ImportLibrary.msp Man page
ImportLibrary.tab Man page
ImportSamples Man page
ImportSamplesFromDir Man page
Intensity Man page
Intensity<- Man page
Intensity<-,tsMSdata-method Man page
Intensity,tsMSdata-method Man page
length,tsLib-method Man page
length,tsSample-method Man page
libData Man page
libData<- Man page
libData<-,tsLib-method Man page
libData,tsLib-method Man page
libId Man page
libId,tsLib-method Man page
libName Man page
libName<- Man page
libName<-,tsLib-method Man page
libName,tsLib-method Man page
libRI Man page
libRI<- Man page
libRI<-,tsLib-method Man page
libRI,tsLib-method Man page
medianRILib Man page
medRI Man page
medRI<- Man page
medRI<-,tsLib-method Man page
medRI,tsLib-method Man page
NetCDFPeakFinding Man page
peakCDFextraction Man page
peakFind Man page
plotAllRIdev Man page
plotAllSpectra Man page
plotFAME Man page
plotPeak Man page
plotPeakSimple Man page
plotRIdev Man page
plotSpectra Man page
Profile Man page
ProfileCleanUp Man page
profileInfo Man page
profileInfo<- Man page
profileInfo<-,tsProfile-method Man page
profileInfo,tsProfile-method Man page
profileInt Man page
profileInt<- Man page
profileInt<-,tsProfile-method Man page
profileInt,tsProfile-method Man page
profileRI Man page
profileRI<- Man page
profileRI<-,tsProfile-method Man page
profileRI,tsProfile-method Man page
profileRT Man page
profileRT<- Man page
profileRT<-,tsProfile-method Man page
profileRT,tsProfile-method Man page
quantMass Man page
quantMass<- Man page
quantMass<-,tsLib-method Man page
quantMass,tsLib-method Man page
quantMatrix Man page
refLib Man page
refLib,tsLib-method Man page
retIndex Man page
retIndex<- Man page
retIndex<-,tsMSdata-method Man page
retIndex,tsMSdata-method Man page
retTime Man page
retTime<- Man page
retTime<-,tsMSdata-method Man page
retTime,tsMSdata-method Man page
ri2rt Man page
RIcorrect Man page
RIdev Man page
RIdev<- Man page
RIdev<-,tsLib-method Man page
RIdev,tsLib-method Man page
RIfiles Man page
RIfiles<- Man page
RIfiles<-,tsSample-method Man page
RIfiles,tsSample-method Man page
riMatrix Man page
rimLimits Man page
rimLimits<- Man page
rimLimits<-,tsRim-method Man page
rimLimits,tsRim-method Man page
rimMass Man page
rimMass<- Man page
rimMass<-,tsRim-method Man page
rimMass,tsRim-method Man page
rimStandard Man page
rimStandard<- Man page
rimStandard<-,tsRim-method Man page
rimStandard,tsRim-method Man page
RIpath Man page
RIpath<- Man page
RIpath<-,tsSample-method Man page
RIpath,tsSample-method Man page
rt2ri Man page
sampleData Man page
sampleData<- Man page
sampleData<-,tsSample-method Man page
sampleData,tsSample-method Man page
sampleDays Man page
sampleDays<- Man page
sampleDays<-,tsSample-method Man page
sampleDays,tsSample-method Man page
sampleNames Man page
sampleNames<- Man page
sampleNames<-,tsSample-method Man page
sampleNames,tsSample-method Man page
sampleRI Man page
selMass Man page
selMass<- Man page
selMass<-,tsLib-method Man page
selMass,tsLib-method Man page
show,tsLib-method Man page
show,tsMSdata-method Man page
show,tsProfile-method Man page
show,tsSample-method Man page
spectra Man page
spectra<- Man page
spectra<-,tsLib-method Man page
spectra,tsLib-method Man page
TargetSearch Man page
TargetSearch-defunct Man page
TargetSearchGUI Man page
TargetSearch-package Man page
text2bin Man page
topMass Man page
topMass<- Man page
topMass<-,tsLib-method Man page
topMass,tsLib-method Man page
tsLib-class Man page
[,tsLib-method Man page
$,tsLib-method Man page
tsMSdata-class Man page
tsProfile-class Man page
tsRim-class Man page
tsSample-class Man page
[,tsSample-method Man page
$,tsSample-method Man page
writeLibText Man page
writeMSP Man page
Write.Results Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.