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:Xavier Domingo-Almenara [aut, cre, cph], Jasen P. Finch [ctb], Adria Olomi [ctb], Sara Samino [aut], Maria Vinaixa [aut], Alexandre Perera [aut, ths], Jesus Brezmes [aut, ths], Oscar Yanes [aut, ths]

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erah.pdf |erah.html✨
erah/json (API)
NEWS

# Install 'erah' in R:
install.packages('erah', repos = c('https://xdomingoal.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/xdomingoal/erah-devel/issues

Datasets:
  • mslib - MassBank Spectral Library

On CRAN:

massspectrometrymetabolomics

4.70 score 5 stars 20 scripts 309 downloads 30 exports 41 dependencies

Last updated 10 months agofrom:6319228133. Checks:OK: 8 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-win-x86_64OKNov 05 2024
R-4.5-linux-x86_64OKNov 05 2024
R-4.4-win-x86_64OKNov 05 2024
R-4.4-mac-x86_64OKNov 05 2024
R-4.4-mac-aarch64OKNov 05 2024
R-4.3-win-x86_64OKNov 05 2024
R-4.3-mac-x86_64OKNov 05 2024
R-4.3-mac-aarch64NOTENov 05 2024

Exports:alignCompalignListcompInfocomputeRIerrorcreatedtcreateInstrumentalTablecreatePhenoTabledataListdeconvolveCompexpClassesexport2CEFexport2MSPfindCompidentifyCompidListimportGMDimportMSPmetaDatanewExpphenoDataplanplotAlignplotChrplotProfileplotSpectrarecMissCompsampleInfosetAlParsetDecParshowRTRICurve

Dependencies:cliclueclustercodetoolscpp11crayondigestfansifurrrfutureglobalsglueHiClimRhmsigraphJADElatticelifecyclelistenvmagrittrMASSMatrixMatrixModelsncdf4nnlsosdparallellypillarpkgconfigprettyunitsprogresspurrrquantregR6rlangsignalSparseMsurvivaltibbleutf8vctrs

eRah Manual

Xavier Domingo–Almenara

Rendered fromerah-manual.Rmdusingknitr::rmarkdownon Nov 05 2024.

Last update: 2024-02-08
Started: 2020-09-09

Readme and manuals

Help Manual

Help pageTopics
Alignment of compoundsalignComp alignComp,MetaboSet-method
Alignment listalignList alignList,MetaboSet-method
Information of a CompoundcompInfo
computeRIerrorcomputeRIerror
Creating Experiment Tablescreatedt
Create Instrumental TablecreateInstrumentalTable
Create Phenotype TablecreatePhenoTable
Data listdataList dataList,MetaboSet-method
Deconvolution of compounds in samplesdeconvolveComp deconvolveComp,MetaboSet-method
Class '"eRah_DB"'eRah_DB-class
expClasses-methodexpClasses expClasses,MetaboSet-method
Export spectra to CEFexport2CEF
Export spectra to MSPexport2MSP
Find a compoundfindComp
Identification of compoundsidentifyComp identifyComp,MetaboSet-method
Identification listidList idList,MetaboSet-method
Import MSP files from GMD to RimportGMD
Import MSP files to RimportMSP
Class '"MetaboSet"'MetaboSet-class
metaData-methodmetaData metaData,MetaboSet-method
MassBank Spectral Librarymslib
New ExperimentnewExp
phenoData-methodphenoData phenoData,MetaboSet-method
Plotting chromatographic profile with and without alignmentplotAlign plotAlign,MetaboSet-method
Plotting sample chromatogramplotChr plotChr,MetaboSet-method
Plotting chromatographic profileplotProfile plotProfile,MetaboSet-method
Plotting SpectraplotSpectra plotSpectra,MetaboSet-method
Class '"RawDataParameters"'RawDataParameters-class
Missing compound recoveryrecMissComp recMissComp,MetaboSet-method
Information of the samplessampleInfo sampleInfo,MetaboSet-method
Set Alignment ParameterssetAlPar
Set Software ParameterssetDecPar
Show MetaboSet objectshow,MetaboSet-method
Show RT-RI curveshowRTRICurve