Package: TargetSearch 2.9.1
Alvaro Cuadros-Inostroza
TargetSearch: A package for the analysis of GC-MS metabolite profiling data
This packages provides a flexible, fast and accurate method for targeted pre-processing of GC-MS data. The user provides a (often very large) set of GC chromatograms and a metabolite library of targets. The package will automatically search those targets in the chromatograms resulting in a data matrix that can be used for further data analysis.
Authors:
TargetSearch_2.9.1.tar.gz
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TargetSearch.pdf |TargetSearch.html✨
TargetSearch/json (API)
NEWS
| # Install 'TargetSearch' in R: |
| install.packages('TargetSearch', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/acinostroza/targetsearch/issues
- RImatrix - Example GC-MS data for TargetSearch Package
- corRI - Example GC-MS data for TargetSearch Package
- metabProfile - Example GC-MS data for TargetSearch Package
- peakData - Example GC-MS data for TargetSearch Package
- refLibrary - Example GC-MS data for TargetSearch Package
- rimLimits - Class for representing retention index markers
- sampleDescription - Example GC-MS data for TargetSearch Package
On BioConductor:TargetSearch-2.9.1(bioc 3.21)TargetSearch-2.8.0(bioc 3.20)
massspectrometrypreprocessingdecisiontreeimmunooncologybiocbioconductorgc-msmass-spectrometry
Last updated 1 months agofrom:5a422d0b70. Checks:OK: 9. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win-x86_64 | OK | Dec 19 2024 |
| R-4.5-linux-x86_64 | OK | Dec 19 2024 |
| R-4.4-win-x86_64 | OK | Dec 19 2024 |
| R-4.4-mac-x86_64 | OK | Dec 19 2024 |
| R-4.4-mac-aarch64 | OK | Dec 19 2024 |
| R-4.3-win-x86_64 | OK | Dec 19 2024 |
| R-4.3-mac-x86_64 | OK | Dec 19 2024 |
| R-4.3-mac-aarch64 | OK | Dec 19 2024 |
Exports:baselinebaselineCorrectionbaselineCorrectionQuantbin2textCDFfilesCDFfiles<-CDFpathCDFpath<-checkRimLimFAMEoutliersfileFormatfileFormat<-FindAllPeaksFindPeaksfixRIfixRIcorrectionImportFameSettingsImportLibraryImportLibrary.mspImportLibrary.tabImportSamplesImportSamplesFromDirIntensityIntensity<-libDatalibData<-libIdlibNamelibName<-libRIlibRI<-makeIndexmedianRILibmedRImedRI<-ncdf4_convertncdf4_convert_from_pathncdf4_data_extractncdf4_plot_peakncdf4_update_rincdf4ConvertNetCDFPeakFindingpeakCDFextractionpeakFindplotAllRIdevplotAllSpectraplotFAMEplotPeakplotPeakRIplotPeakSimpleplotRefSpectraplotRIdevplotSpectraProfileProfileCleanUpprofileInfoprofileInfo<-profileIntprofileInt<-profileRIprofileRI<-profileRTprofileRT<-quantMassquantMass<-quantMatrixrefLibretIndexretIndex<-retTimeretTime<-ri_data_extractri_plot_peakri2rtRIcorrectRIdevRIdev<-RIfilesRIfiles<-riMatrixrimLimitsrimLimits<-rimMassrimMass<-rimStandardrimStandard<-RIpathRIpath<-rt2risampleDatasampleData<-sampleDayssampleDays<-sampleNamessampleNames<-sampleRIselMassselMass<-showspectraspectra<-TargetSearchGUItext2bintopMasstopMass<-tsUpdateupdateRIWrite.ResultswriteLibTextwriteMSP
Dependencies:assertthatncdf4
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| A targeted approach for GC-MS data. | TargetSearch-package TargetSearch |
| Baseline correction - wrapper function | baseline |
| Baseline correction - Chang's method | baselineCorrection |
| Baseline correction - quantiles method | baselineCorrectionQuant |
| Visually check retention index marker limits | checkRimLim |
| FAME outlier detection | FAMEoutliers |
| Extract peaks from chromatogram files - low level function | FindAllPeaks |
| Extract peaks from chromatogram files | FindPeaks |
| Fixing Retention Time Index Correction | fixRI |
| Retention time markers settings | ImportFameSettings |
| Library import | ImportLibrary ImportLibrary.msp ImportLibrary.tab |
| Sample definitions | ImportSamples ImportSamplesFromDir |
| Make an index vector out of selective/top masses | makeIndex |
| Median RI library correction | medianRILib |
| Convert from a NetCDF file format 3 to format 4 | ncdf4_convert |
| Convert CDF files to CDF4 from a path automatically | ncdf4_convert_from_path |
| Extract data ranges from a NetCDF file format 4 | ncdf4_data_extract |
| Plot peaks from ncdf4 files | ncdf4_plot_peak |
| Update retention time index on a NCDF4 file | ncdf4_update_ri |
| Method for converting CDF-3 files to CDF-4 | ncdf4Convert ncdf4Convert,tsSample-method |
| Peak picking algorithm from CDF files | NetCDFPeakFinding |
| NetCDF to R | peakCDFextraction |
| Intensities and RI matrices | peakFind |
| Plot a standard marker | plotFAME |
| Plot peaks | plotPeak |
| Plot peak RI across samples | plotPeakRI |
| Plot peaks - simple (old) interface | plotPeakSimple |
| Plot reference spectrum of a compound | plotRefSpectra |
| Plot Retention Time Index Deviation | plotAllRIdev plotRIdev |
| Plot a Spectra Comparison | plotAllSpectra plotSpectra |
| Average the correlating masses for each metabolite | Profile |
| Reduce redundancy of the profile | ProfileCleanUp |
| Create an intensity matrix using quantification masses | quantMatrix |
| Extract peak data from a RI file | ri_data_extract |
| Plot peak RI across samples - low level interface | ri_plot_peak |
| Retention Time Index to Retention Time conversion | ri2rt |
| Peak picking from CDF files and RI correction | RIcorrect |
| Retention Time Index Matrix | riMatrix |
| Retention Time to Retention Time Index conversion | rt2ri |
| Sample specific RI detection | sampleRI |
| Defunct functions in package 'TargetSearch' | fixRIcorrection fixRIcorrection-defunct TargetSearch-defunct TargetSearchGUI |
| Deprecated functions in package 'TargetSearch' | TargetSearch-deprecated |
| Convert RI files from text to binary format and vice versa | bin2text text2bin |
| Example GC-MS data for TargetSearch Package | corRI metabProfile peakData refLibrary RImatrix sampleDescription TSExample |
| Class for representing a reference library | $,tsLib-method c,tsLib-method length,tsLib-method libData libData,tsLib-method libData<- libData<-,tsLib-method libId libId,tsLib-method libName libName,tsLib-method libName<- libName<-,tsLib-method libRI libRI,tsLib-method libRI<- libRI<-,tsLib-method medRI medRI,tsLib-method medRI<- medRI<-,tsLib-method quantMass quantMass,tsLib-method quantMass<- quantMass<-,tsLib-method refLib refLib,tsLib-method RIdev RIdev,tsLib-method RIdev<- RIdev<-,tsLib-method selMass selMass,tsLib-method selMass<- selMass<-,tsLib-method show,tsLib-method spectra spectra,tsLib-method spectra<- spectra<-,tsLib-method topMass topMass,tsLib-method topMass<- topMass<-,tsLib-method tsLib-class [,tsLib-method |
| Class for representing MS data | as.list,tsMSdata-method as.list.tsMSdata as.list.tsMSdata,tsMSdata-method as.list.tsProfile as.list.tsProfile,tsMSdata-method Intensity Intensity,tsMSdata-method Intensity<- Intensity<-,tsMSdata-method retIndex retIndex,tsMSdata-method retIndex<- retIndex<-,tsMSdata-method retTime retTime,tsMSdata-method retTime<- retTime<-,tsMSdata-method show,tsMSdata-method tsMSdata-class |
| Class for representing a MS profile | profileInfo profileInfo,tsProfile-method profileInfo<- profileInfo<-,tsProfile-method profileInt profileInt,tsProfile-method profileInt<- profileInt<-,tsProfile-method profileRI profileRI,tsProfile-method profileRI<- profileRI<-,tsProfile-method profileRT profileRT,tsProfile-method profileRT<- profileRT<-,tsProfile-method show,tsProfile-method tsProfile-class |
| Class for representing retention index markers | c,tsRim-method length,tsRim-method rimLimits rimLimits,tsRim-method rimLimits<- rimLimits<-,tsRim-method rimMass rimMass,tsRim-method rimMass<- rimMass<-,tsRim-method rimStandard rimStandard,tsRim-method rimStandard<- rimStandard<-,tsRim-method tsRim-class [,tsRim-method |
| Class for representing samples | $,tsSample-method c,tsSample-method CDFfiles CDFfiles,tsSample-method CDFfiles<- CDFfiles<-,tsSample-method CDFpath CDFpath,tsSample-method CDFpath<- CDFpath<-,tsSample-method fileFormat fileFormat,tsSample-method fileFormat<- fileFormat<-,tsSample-method length,tsSample-method RIfiles RIfiles,tsSample-method RIfiles<- RIfiles<-,tsSample-method RIpath RIpath,tsSample-method RIpath<- RIpath<-,tsSample-method sampleData sampleData,tsSample-method sampleData<- sampleData<-,tsSample-method sampleDays sampleDays,tsSample-method sampleDays<- sampleDays<-,tsSample-method sampleNames sampleNames,tsSample-method sampleNames<- sampleNames<-,tsSample-method show,tsSample-method tsSample-class [,tsSample-method |
| Methods for Updating TargetSearch objects 'tsUpdate' | tsUpdate tsUpdate,tsSample-method |
| Updating Time Index correction | updateRI |
| Save TargetSearch result objects into files | Write.Results |
| Save a library object in text format | writeLibText |
| Save spectra in MSP format to be visualized in NIST | writeMSP |
