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]

erah_2.0.0.tar.gz
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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

Datasets:

mslib - MassBank Spectral Library

On CRAN:

massspectrometry metabolomics

5.19 score 6 stars 26 scripts 312 downloads 30 exports 40 dependencies

Last updated from:6319228133. Checks:13 OK. Indexed: yes.

Target	Result	Time
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:alignComp alignList compInfo computeRIerror createdt createInstrumentalTable createPhenoTable dataList deconvolveComp expClasses export2CEF export2MSP findComp identifyComp idList importGMD importMSP metaData newExp phenoData plan plotAlign plotChr plotProfile plotSpectra recMissComp sampleInfo setAlPar setDecPar showRTRICurve

Dependencies:cli clue cluster codetools cpp11 crayon digest furrr future globals glue HiClimR hms igraph JADE lattice lifecycle listenv magrittr MASS Matrix MatrixModels ncdf4 nnls osd parallelly pillar pkgconfig prettyunits progress purrr quantreg R6 rlang signal SparseM survival tibble utf8 vctrs

eRah Manual

Installation | Support

Rendered fromerah-manual.Rmdusingknitr::rmarkdown

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

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

Package: erah 2.0.0

erah: Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics

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