Package: erah 2.0.0
erah: Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics
Automated compound deconvolution, alignment across samples, and identification of metabolites by spectral library matching in Gas Chromatography - Mass spectrometry (GC-MS) untargeted metabolomics. Outputs a table with compound names, matching scores and the integrated area of the compound for each sample. Package implementation is described in Domingo-Almenara et al. (2016) <doi:10.1021/acs.analchem.6b02927>.
Authors:
erah_2.0.0.tar.gz
erah_2.0.0.zip(r-4.7)erah_2.0.0.zip(r-4.6)erah_2.0.0.zip(r-4.5)
erah_2.0.0.tgz(r-4.6-x86_64)erah_2.0.0.tgz(r-4.6-arm64)erah_2.0.0.tgz(r-4.5-x86_64)erah_2.0.0.tgz(r-4.5-arm64)
erah_2.0.0.tar.gz(r-4.7-arm64)erah_2.0.0.tar.gz(r-4.7-x86_64)erah_2.0.0.tar.gz(r-4.6-arm64)erah_2.0.0.tar.gz(r-4.6-x86_64)
erah_2.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
erah/json (API)
| # Install 'erah' in R: |
| install.packages('erah', repos = c('https://xdomingoal.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/xdomingoal/erah-devel/issues
Pkgdown/docs site:https://xdomingoal.github.io
- mslib - MassBank Spectral Library
Last updated from:6319228133. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 228 | ||
| linux-devel-x86_64 | OK | 211 | ||
| source / vignettes | OK | 326 | ||
| linux-release-arm64 | OK | 251 | ||
| linux-release-x86_64 | OK | 179 | ||
| macos-release-arm64 | OK | 166 | ||
| macos-release-x86_64 | OK | 378 | ||
| macos-oldrel-arm64 | OK | 138 | ||
| macos-oldrel-x86_64 | OK | 477 | ||
| windows-devel | OK | 158 | ||
| windows-release | OK | 149 | ||
| windows-oldrel | OK | 177 | ||
| wasm-release | OK | 165 |
Exports:alignCompalignListcompInfocomputeRIerrorcreatedtcreateInstrumentalTablecreatePhenoTabledataListdeconvolveCompexpClassesexport2CEFexport2MSPfindCompidentifyCompidListimportGMDimportMSPmetaDatanewExpphenoDataplanplotAlignplotChrplotProfileplotSpectrarecMissCompsampleInfosetAlParsetDecParshowRTRICurve
Dependencies:cliclueclustercodetoolscpp11crayondigestfurrrfutureglobalsglueHiClimRhmsigraphJADElatticelifecyclelistenvmagrittrMASSMatrixMatrixModelsncdf4nnlsosdparallellypillarpkgconfigprettyunitsprogresspurrrquantregR6rlangsignalSparseMsurvivaltibbleutf8vctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Alignment of compounds | alignComp alignComp,MetaboSet-method |
| Alignment list | alignList alignList,MetaboSet-method |
| Information of a Compound | compInfo |
| computeRIerror | computeRIerror |
| Creating Experiment Tables | createdt |
| Create Instrumental Table | createInstrumentalTable |
| Create Phenotype Table | createPhenoTable |
| Data list | dataList dataList,MetaboSet-method |
| Deconvolution of compounds in samples | deconvolveComp deconvolveComp,MetaboSet-method |
| Class '"eRah_DB"' | eRah_DB-class |
| expClasses-method | expClasses expClasses,MetaboSet-method |
| Export spectra to CEF | export2CEF |
| Export spectra to MSP | export2MSP |
| Find a compound | findComp |
| Identification of compounds | identifyComp identifyComp,MetaboSet-method |
| Identification list | idList idList,MetaboSet-method |
| Import MSP files from GMD to R | importGMD |
| Import MSP files to R | importMSP |
| Class '"MetaboSet"' | MetaboSet-class |
| metaData-method | metaData metaData,MetaboSet-method |
| MassBank Spectral Library | mslib |
| New Experiment | newExp |
| phenoData-method | phenoData phenoData,MetaboSet-method |
| Plotting chromatographic profile with and without alignment | plotAlign plotAlign,MetaboSet-method |
| Plotting sample chromatogram | plotChr plotChr,MetaboSet-method |
| Plotting chromatographic profile | plotProfile plotProfile,MetaboSet-method |
| Plotting Spectra | plotSpectra plotSpectra,MetaboSet-method |
| Class '"RawDataParameters"' | RawDataParameters-class |
| Missing compound recovery | recMissComp recMissComp,MetaboSet-method |
| Information of the samples | sampleInfo sampleInfo,MetaboSet-method |
| Set Alignment Parameters | setAlPar |
| Set Software Parameters | setDecPar |
| Show MetaboSet object | show,MetaboSet-method |
| Show RT-RI curve | showRTRICurve |
