erah: Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics
Version 1.0.5

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.

AuthorXavier Domingo-Almenara, Sara Samino, Maria Vinaixa, Alexandre Perera, Oscar Yanes
Date of publication2017-01-14 01:53:04
MaintainerXavier Domingo-Almenara <xdomingo@scripps.edu>
LicenseGPL (>= 2)
Version1.0.5
URL http://metabolomicsplatform.com/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("erah")

Popular man pages

findComp: Find a Compound
importMSP: Import MSP files to R
metaData: Metadata
mslib: MassBank Spectral Library
phenoData: Show Phenotyphe data
plotChr: Plotting sample chromatogram
setDecPar: Set Software Parameters
See all...

All man pages Function index File listing

Man pages

alignComp: Alignment of compounds
alignList: Alignment list
compInfo: Information of a Compound
createdt: Creating Experiment Tables
dataList: Data list
deconvolveComp: Deconvolution of compounds in samples
eRah_DB-class: Class '"eRah_DB"'
expClasses: Experiment classes
export2CEF: Export spectra to CEF
export2MSP: Export spectra to MSP
findComp: Find a Compound
identifyComp: Identification of compounds
idList: Identification list
importGMD: Import MSP files from GMD to R
importMSP: Import MSP files to R
MetaboSet-class: Class '"MetaboSet"'
metaData: Metadata
mslib: MassBank Spectral Library
newExp: New Experiment
phenoData: Show Phenotyphe data
plotAlign: Plotting chromatophic profile with and without alignement
plotChr: Plotting sample chromatogram
plotProfile: Plotting chromatophic profile
plotSpectra: Plotting spectra
RawDataParameters-class: Class '"RawDataParameters"'
recMissComp: Missing compound recovery
sampleInfo: Information of the samples
setAlPar: Set Alignment Parameters
setDecPar: Set Software Parameters
show.MetaboSet: Show MetaboSet object

Functions

MetaboSet-class Man page
RawDataParameters-class Man page
align.factors Source code
alignComp Man page Source code
alignList Man page Source code
avoid.processing Source code
break.vector Source code
chrom.isoreg Source code
comp.clusters Source code
compInfo Man page Source code
convertMSPspectra Source code
convertMSPspectra.dot Source code
cor.sinus Source code
create.factorlist.table Source code
createdt Man page Source code
dataList Man page Source code
deconvolveComp Man page Source code
eRah_DB-class Man page
expClasses Man page Source code
export2CEF Man page Source code
export2MSP Man page Source code
findComp Man page Source code
fit.model.in.data.tosd Source code
get.compound.info_GMD Source code
get.compound.info_MSP Source code
get.factor.list Source code
get.max.sign Source code
get.nrowcol Source code
get.spectra.matrix Source code
getC.rq Source code
getC.tP Source code
getS.OSD Source code
idList Man page Source code
identify.factors Source code
identifyComp Man page Source code
importGMD Man page Source code
importMSP Man page Source code
is.even Source code
lagFFT Source code
list.DB Source code
load.erahrd Source code
load.file Source code
load.ncdf4 Source code
load.xml Source code
log.error Source code
metaData Man page Source code
mslib Man page
newExp Man page Source code
onAttach Source code
paste.sp Source code
phenoData Man page Source code
plotAlign Man page Source code
plotChr Man page Source code
plotProfile Man page Source code
plotSpectra Man page Source code
pre.process Source code
processSample Source code
recMissComp Man page Source code
refine.extraction Source code
removeBaseline Source code
sampleInfo Man page Source code
setAlPar Man page Source code
setDBinMemory Source code
setDecPar Man page Source code
show.MetaboSet Man page
soft.filter Source code
sparse.to.vector Source code

Files

inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/eRahManual.pdf
inst/doc/eRahManual.pdf.asis
NAMESPACE
data
data/mslib.rda
R
R/preprocessing.R
R/plotting.R
R/alignment.R
R/identification.R
R/erah.R
R/processing.R
R/missingCompRecovery.R
R/MSimport.R
R/DB.R
R/file.R
R/support.R
R/support_methods.R
R/MSexport.R
R/zzz.R
vignettes
vignettes/eRahManual.pdf.asis
MD5
build
build/vignette.rds
DESCRIPTION
man
man/dataList.Rd
man/export2MSP.Rd
man/MetaboSet-class.Rd
man/setDecPar.Rd
man/metaData.Rd
man/show.MetaboSet.Rd
man/plotProfile.Rd
man/deconvolveComp.Rd
man/mslib.Rd
man/compInfo.Rd
man/newExp.Rd
man/plotAlign.Rd
man/sampleInfo.Rd
man/importGMD.Rd
man/createdt.Rd
man/alignComp.Rd
man/eRah_DB-class.Rd
man/idList.Rd
man/expClasses.Rd
man/identifyComp.Rd
man/phenoData.Rd
man/RawDataParameters-class.Rd
man/findComp.Rd
man/recMissComp.Rd
man/alignList.Rd
man/export2CEF.Rd
man/setAlPar.Rd
man/plotSpectra.Rd
man/plotChr.Rd
man/importMSP.Rd
erah documentation built on May 19, 2017, 6:27 p.m.

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