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erah (version 2.0.1)

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

Description

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) .

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Version

Install

install.packages('erah')

Monthly Downloads

318

Version

2.0.1

License

GPL (>= 2)

Last Published

December 20th, 2023

Functions in erah (2.0.1)

createdt

Creating Experiment Tables
dataList

Data list
expClasses

expClasses-method
export2CEF

Export spectra to CEF
plotProfile

Plotting chromatographic profile
plotSpectra

Plotting Spectra
showRTRICurve

Show RT-RI curve
MetaboSet-class

Class "MetaboSet"
RawDataParameters-class

Class "RawDataParameters"
export2MSP

Export spectra to MSP
findComp

Find a compound
alignComp

Alignment of compounds
alignList

Alignment list
newExp

New Experiment
phenoData

phenoData-method
deconvolveComp

Deconvolution of compounds in samples
eRah_DB-class

Class "eRah_DB"
plotAlign

Plotting chromatographic profile with and without alignment
plotChr

Plotting sample chromatogram
sampleInfo

Information of the samples
setAlPar

Set Alignment Parameters
createInstrumentalTable

Create Instrumental Table
createPhenoTable

Create Phenotype Table
idList

Identification list
identifyComp

Identification of compounds
metaData

metaData-method
mslib

MassBank Spectral Library
compInfo

Information of a Compound
computeRIerror

computeRIerror
importGMD

Import MSP files from GMD to R
importMSP

Import MSP files to R
recMissComp

Missing compound recovery
reexports

Objects exported from other packages
setDecPar

Set Software Parameters
show,MetaboSet-method

Show MetaboSet object