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


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Documentation for package ‘TargetSearch’ version 2.6.0

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

TargetSearch-package A targeted approach for GC-MS data.

-- A --

as.list-method Class for representing MS data
as.list.tsMSdata Class for representing MS data
as.list.tsMSdata-method Class for representing MS data
as.list.tsProfile Class for representing MS data
as.list.tsProfile-method Class for representing MS data

-- B --

baseline Baseline correction - wrapper function
baselineCorrection Baseline correction - Chang's method
baselineCorrectionQuant Baseline correction - quantiles method
bin2text Convert RI files from text to binary format and vice versa

-- C --

c-method Class for representing a reference library
c-method Class for representing retention index markers
c-method Class for representing samples
CDFfiles Class for representing samples
CDFfiles-method Class for representing samples
CDFfiles<- Class for representing samples
CDFfiles<--method Class for representing samples
CDFpath Class for representing samples
CDFpath-method Class for representing samples
CDFpath<- Class for representing samples
CDFpath<--method Class for representing samples
checkRimLim Visually check retention index marker limits
corRI Example GC-MS data for TargetSearch Package

-- F --

FAMEoutliers FAME outlier detection
fileFormat Class for representing samples
fileFormat-method Class for representing samples
fileFormat<- Class for representing samples
fileFormat<--method Class for representing samples
FindAllPeaks Extract peaks from chromatogram files - low level function
FindPeaks Extract peaks from chromatogram files
fixRI Fixing Retention Time Index Correction
fixRIcorrection Defunct functions in package 'TargetSearch'
fixRIcorrection-defunct Defunct functions in package 'TargetSearch'

-- I --

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

-- L --

length-method Class for representing a reference library
length-method Class for representing retention index markers
length-method Class for representing samples
libData Class for representing a reference library
libData-method Class for representing a reference library
libData<- Class for representing a reference library
libData<--method Class for representing a reference library
libId Class for representing a reference library
libId-method Class for representing a reference library
libName Class for representing a reference library
libName-method Class for representing a reference library
libName<- Class for representing a reference library
libName<--method Class for representing a reference library
libRI Class for representing a reference library
libRI-method Class for representing a reference library
libRI<- Class for representing a reference library
libRI<--method Class for representing a reference library

-- M --

medianRILib Median RI library correction
medRI Class for representing a reference library
medRI-method Class for representing a reference library
medRI<- Class for representing a reference library
medRI<--method Class for representing a reference library
metabProfile Example GC-MS data for TargetSearch Package

-- N --

ncdf4Convert Method for converting CDF-3 files to CDF-4
ncdf4Convert-method Method for converting CDF-3 files to CDF-4
ncdf4_convert Convert from a NetCDF file format 3 to format 4
ncdf4_convert_from_path Convert CDF files to CDF4 from a path automatically
ncdf4_data_extract Extract data ranges from a NetCDF file format 4
ncdf4_plot_peak Plot peaks from ncdf4 files
ncdf4_update_ri Update retention time index on a NCDF4 file
NetCDFPeakFinding Peak picking algorithm from CDF files

-- P --

peakCDFextraction NetCDF to R
peakData Example GC-MS data for TargetSearch Package
peakFind Intensities and RI matrices
plotAllRIdev Plot Retention Time Index Deviation
plotAllSpectra Plot a Spectra Comparison
plotFAME Plot a standard marker
plotPeak Plot peaks
plotPeakRI Plot peak RI across samples
plotPeakSimple Plot peaks - simple (old) interface
plotRefSpectra Plot reference spectrum of a compound
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-method Class for representing a MS profile
profileInfo<- Class for representing a MS profile
profileInfo<--method Class for representing a MS profile
profileInt Class for representing a MS profile
profileInt-method Class for representing a MS profile
profileInt<- Class for representing a MS profile
profileInt<--method Class for representing a MS profile
profileRI Class for representing a MS profile
profileRI-method Class for representing a MS profile
profileRI<- Class for representing a MS profile
profileRI<--method Class for representing a MS profile
profileRT Class for representing a MS profile
profileRT-method Class for representing a MS profile
profileRT<- Class for representing a MS profile
profileRT<--method Class for representing a MS profile

-- Q --

quantMass Class for representing a reference library
quantMass-method Class for representing a reference library
quantMass<- Class for representing a reference library
quantMass<--method Class for representing a reference library
quantMatrix Create an intensity matrix using quantification masses

-- R --

refLib Class for representing a reference library
refLib-method Class for representing a reference library
refLibrary Example GC-MS data for TargetSearch Package
retIndex Class for representing MS data
retIndex-method Class for representing MS data
retIndex<- Class for representing MS data
retIndex<--method Class for representing MS data
retTime Class for representing MS data
retTime-method Class for representing MS data
retTime<- Class for representing MS data
retTime<--method Class for representing MS data
ri2rt Retention Time Index to Retention Time conversion
RIcorrect Peak picking from CDF files and RI correction
RIdev Class for representing a reference library
RIdev-method Class for representing a reference library
RIdev<- Class for representing a reference library
RIdev<--method Class for representing a reference library
RIfiles Class for representing samples
RIfiles-method Class for representing samples
RIfiles<- Class for representing samples
RIfiles<--method Class for representing samples
RImatrix Example GC-MS data for TargetSearch Package
riMatrix Retention Time Index Matrix
rimLimits Class for representing retention index markers
rimLimits-method Class for representing retention index markers
rimLimits<- Class for representing retention index markers
rimLimits<--method Class for representing retention index markers
rimMass Class for representing retention index markers
rimMass-method Class for representing retention index markers
rimMass<- Class for representing retention index markers
rimMass<--method Class for representing retention index markers
rimStandard Class for representing retention index markers
rimStandard-method Class for representing retention index markers
rimStandard<- Class for representing retention index markers
rimStandard<--method Class for representing retention index markers
RIpath Class for representing samples
RIpath-method Class for representing samples
RIpath<- Class for representing samples
RIpath<--method Class for representing samples
ri_data_extract Extract peak data from a RI file
ri_plot_peak Plot peak RI across samples - low level interface
rt2ri Retention Time to Retention Time Index conversion

-- S --

sampleData Class for representing samples
sampleData-method Class for representing samples
sampleData<- Class for representing samples
sampleData<--method Class for representing samples
sampleDays Class for representing samples
sampleDays-method Class for representing samples
sampleDays<- Class for representing samples
sampleDays<--method Class for representing samples
sampleDescription Example GC-MS data for TargetSearch Package
sampleNames Class for representing samples
sampleNames-method Class for representing samples
sampleNames<- Class for representing samples
sampleNames<--method Class for representing samples
sampleRI Sample specific RI detection
selMass Class for representing a reference library
selMass-method Class for representing a reference library
selMass<- Class for representing a reference library
selMass<--method Class for representing a reference library
show-method Class for representing a reference library
show-method Class for representing MS data
show-method Class for representing a MS profile
show-method Class for representing samples
spectra Class for representing a reference library
spectra-method Class for representing a reference library
spectra<- Class for representing a reference library
spectra<--method Class for representing a reference library

-- T --

TargetSearch A targeted approach for GC-MS data.
TargetSearch-defunct Defunct functions in package 'TargetSearch'
TargetSearchGUI Defunct functions in package 'TargetSearch'
text2bin Convert RI files from text to binary format and vice versa
topMass Class for representing a reference library
topMass-method Class for representing a reference library
topMass<- Class for representing a reference library
topMass<--method Class for representing a reference library
TSExample Example GC-MS data for TargetSearch Package
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
tsUpdate Methods for Updating TargetSearch objects 'tsUpdate'
tsUpdate-method Methods for Updating TargetSearch objects 'tsUpdate'

-- U --

updateRI Updating Time Index correction

-- W --

Write.Results Save TargetSearch result objects into files
writeLibText Save a library object in text format
writeMSP Save spectra in MSP format to be visualized in NIST

-- misc --

$-method Class for representing a reference library
$-method Class for representing samples
[-method Class for representing a reference library
[-method Class for representing retention index markers
[-method Class for representing samples