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


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Documentation for package ‘TargetSearch’ version 1.2.0

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B C F I L M N P R S T W misc

-- --

$,tsLib-method Class for representing a reference library
$,tsSample-method Class for representing samples

-- B --

baseline Baseline correction algorithm
baselineCorrection Baseline correction algorithm

-- C --

CDFfiles Class for representing samples
CDFfiles,tsSample-method Class for representing samples
CDFfiles<- Class for representing samples
CDFfiles<-,tsSample-method Class for representing samples
CDFpath Class for representing samples
CDFpath,tsSample-method Class for representing samples
CDFpath<- Class for representing samples
CDFpath<-,tsSample-method Class for representing samples

-- F --

FAMEoutliers FAME outlier detection
FindPeaks Extract peaks from chromatogram files
fixRIcorrection Manual Retention Time Index Correction

-- I --

ImportFameSettings Retention time markers settings
ImportLibrary Library import
ImportLibrary.msp Library import
ImportLibrary.tab Library import
ImportSamples Sample definitions
Intensity Class for representing MS data
Intensity,tsMSdata-method Class for representing MS data
Intensity<- Class for representing MS data
Intensity<-,tsMSdata-method Class for representing MS data

-- L --

length,tsLib-method Class for representing a reference library
length,tsSample-method Class for representing samples
libData Class for representing a reference library
libData,tsLib-method Class for representing a reference library
libId Class for representing a reference library
libId,tsLib-method Class for representing a reference library
libName Class for representing a reference library
libName,tsLib-method Class for representing a reference library
libName<- Class for representing a reference library
libName<-,tsLib-method Class for representing a reference library
libRI Class for representing a reference library
libRI,tsLib-method Class for representing a reference library
libRI<- Class for representing a reference library
libRI<-,tsLib-method Class for representing a reference library

-- M --

medianRILib Median RI library correction
medRI Class for representing a reference library
medRI,tsLib-method Class for representing a reference library
medRI<- Class for representing a reference library
medRI<-,tsLib-method Class for representing a reference library

-- N --

NetCDFPeakFinding Peak picking algorithm from CDF files

-- P --

peakCDFextraction NetCDF to R
peakFind Intensities and RI matrices
plotAllRIdev Plot Retention Time Index Deviation
plotAllSpectra Plot a Spectra Comparison
plotFAME Plot a standard marker
plotPeak Plot peaks
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
profileInfo Class for representing a MS profile
profileInfo,tsProfile-method Class for representing a MS profile
profileInfo<- Class for representing a MS profile
profileInfo<-,tsProfile-method Class for representing a MS profile

-- R --

refLib Class for representing a reference library
refLib,tsLib-method Class for representing a reference library
retIndex Class for representing MS data
retIndex,tsMSdata-method Class for representing MS data
retIndex<- Class for representing MS data
retIndex<-,tsMSdata-method Class for representing MS data
retTime Class for representing MS data
retTime,tsMSdata-method Class for representing MS data
retTime<- Class for representing MS data
retTime<-,tsMSdata-method Class for representing MS data
ri2rt Retention Time Index to Retention Time convertion
RIcorrect Peak picking from CDF files and RI correction
RIdev Class for representing a reference library
RIdev,tsLib-method Class for representing a reference library
RIdev<- Class for representing a reference library
RIdev<-,tsLib-method Class for representing a reference library
RIfiles Class for representing samples
RIfiles,tsSample-method Class for representing samples
RIfiles<- Class for representing samples
RIfiles<-,tsSample-method Class for representing samples
rimLimits Class for representing retention index markers
rimLimits,tsRim-method Class for representing retention index markers
rimLimits<- Class for representing retention index markers
rimLimits<-,tsRim-method Class for representing retention index markers
rimMass Class for representing retention index markers
rimMass,tsRim-method Class for representing retention index markers
rimMass<- Class for representing retention index markers
rimMass<-,tsRim-method Class for representing retention index markers
rimStandard Class for representing retention index markers
rimStandard,tsRim-method Class for representing retention index markers
rimStandard<- Class for representing retention index markers
rimStandard<-,tsRim-method Class for representing retention index markers
RIpath Class for representing samples
RIpath,tsSample-method Class for representing samples
RIpath<- Class for representing samples
RIpath<-,tsSample-method Class for representing samples
rt2ri Retention Time to Retention Time Index convertion

-- S --

sampleData Class for representing samples
sampleData,tsSample-method Class for representing samples
sampleDays Class for representing samples
sampleDays,tsSample-method Class for representing samples
sampleDays<- Class for representing samples
sampleDays<-,tsSample-method Class for representing samples
sampleNames Class for representing samples
sampleNames,tsSample-method Class for representing samples
sampleNames<- Class for representing samples
sampleNames<-,tsSample-method Class for representing samples
sampleRI Sample especific RI detection
selMass Class for representing a reference library
selMass,tsLib-method Class for representing a reference library
selMass<- Class for representing a reference library
selMass<-,tsLib-method Class for representing a reference library
show,tsLib-method Class for representing a reference library
show,tsMSdata-method Class for representing MS data
show,tsProfile-method Class for representing a MS profile
show,tsSample-method Class for representing samples
spectra Class for representing a reference library
spectra,tsLib-method Class for representing a reference library
spectra<- Class for representing a reference library
spectra<-,tsLib-method Class for representing a reference library

-- T --

TargetSearch A targeted approach for GC-MS data.
TargetSearchGUI A GUI for TargetSearch
topMass Class for representing a reference library
topMass,tsLib-method Class for representing a reference library
topMass<- Class for representing a reference library
topMass<-,tsLib-method Class for representing a reference library
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

-- W --

Write.Results Save TargetSearch result objects into files
writeMSP Save spectra in MSP format to be visualized in NIST

-- misc --

[,tsLib-method Class for representing a reference library
[,tsSample-method Class for representing samples