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

## Documentation for package ‘TargetSearch’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
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 convertion
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 convertion

## -- 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