metaX: An R package for metabolomic data analysis
Version 1.4.2

The package provides a integrated pipeline for mass spectrometry- based metabolomic data analysis. It includes the stages peak detection, data preprocessing, normalization, missing value imputation, univariate statistical analysis, multivariate statistical analysis such as PCA and PLS-DA, metabolite identification, pathway analysis, power analysis, feature selection and modeling, data quality assessment.

Browse man pages Browse package API and functions Browse package files

AuthorBo Wen <wenbo@genomics.cn>
Date of publicationNone
MaintainerBo Wen <wenbo@genomics.cn>
LicenseLGPL-2
Version1.4.2
URL http://wenbostar.github.io/metaX/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("metaX")

Man pages

addIdentInfo: Add identification result into metaXpara object
addValueNorm: addValueNorm
autoRemoveOutlier: Automatically detect outlier samples
bootPLSDA: Fit predictive models for PLS-DA
calcAUROC: Classical univariate ROC analysis
calcVIP: Calculate the VIP for PLS-DA
center: center
checkPvaluePlot: checkPvaluePlot
checkQCPlot: checkQCPlot
cor.network: Correlation network analysis
createModels: Create predictive models
dataClean: dataClean
dir.case: dir.case
dir.ctrl: dir.ctrl
doQCRLSC: Using the QC samples to do the quality control-robust spline...
featureSelection: Feature selection and modeling
filterPeaks: filterPeaks
filterQCPeaks: filterQCPeaks
filterQCPeaksByCV: Filter peaks according to the RSD of peaks in QC samples
getPeaksTable: Get a data.frame which contained the peaksData in metaXpara
group.bw: group.bw
group.bw0: group.bw0
group.max: group.max
group.minfrac: group.minfrac
group.minsamp: group.minsamp
group.mzwid: group.mzwid
group.mzwid0: group.mzwid0
group.sleep: group.sleep
hasQC: Judge whether the data has QC samples
idres: idres
importDataFromMetaboAnalyst: importDataFromMetaboAnalyst
importDataFromQI: importDataFromQI
importDataFromXCMS: importDataFromXCMS
kfold: kfold
makeDirectory: Create directory
makeMetaboAnalystInput: Export a csv file which can be used for MetaboAnalyst
metaboliteAnnotation: Metabolite identification
metaXpara-class: An S4 class to represent the parameters and data for data...
metaXpipe: metaXpipe
method: method
missingValueImpute: Missing value imputation
missValueImputeMethod: missValueImputeMethod
myCalcAUROC: Classical univariate ROC analysis
myPLSDA: Perform PLS-DA analysis
ncomp: ncomp
normalize: Normalisation of peak intensity
nperm: nperm
outdir: outdir
pathwayAnalysis: Pathway analysis
peakFinder: Peak detection by using XCMS package
peaksData: peaksData
peakStat: Do the univariate and multivariate statistical analysis
permutePLSDA: permutePLSDA
plotCorHeatmap: Plot correlation heatmap
plotCV: Plot the CV distribution of peaks in each group
plotHeatMap: Plot heatmap
plotIntDistr: Plot the distribution of the peaks intensity
plotLoading: Plot figures for PCA/PLS-DA loadings
plotMissValue: Plot missing value distribution
plotNetwork: Plot correlation network map
plotPCA: Plot PCA figure
plotPeakBox: Plot boxplot for each feature
plotPeakNumber: Plot the distribution of the peaks number
plotPeakSN: Plot the distribution of the peaks S/N
plotPeakSumDist: Plot the total peak intensity distribution
plotPLSDA: Plot PLS-DA figure
plotQC: Plot the correlation change of the QC samples.
plotQCRLSC: Plot figures for QC-RLSC
plotTreeMap: Plot Phylogenies for samples
plsDAPara-class: An S4 class to represent the parameters for PLS-DA analysis
powerAnalyst: Power Analysis
prefix: prefix
preProcess: Pre-Processing
qcRlscSpan: qcRlscSpan
ratioPairs: ratioPairs
rawPeaks: rawPeaks
removeSample: Remove samples from the metaXpara object
reSetPeaksData: reSetPeaksData
retcor.method: retcor.method
retcor.plottype: retcor.plottype
retcor.profStep: retcor.profStep
runPLSDA: runPLSDA
sampleListFile: sampleListFile
scale: scale
selectBestComponent: Select the best component for PLS-DA
t: t
transformation: Data transformation
validation: validation
xcmsSet.fitgauss: xcmsSet.fitgauss
xcmsSet.fwhm: xcmsSet.fwhm
xcmsSet.integrate: xcmsSet.integrate
xcmsSet.max: xcmsSet.max
xcmsSet.method: xcmsSet.method
xcmsSet.mzCenterFun: xcmsSet.mzCenterFun
xcmsSet.mzdiff: xcmsSet.mzdiff
xcmsSet.noise: xcmsSet.noise
xcmsSet.nSlaves: xcmsSet.nSlaves
xcmsSetObj: xcmsSetObj
xcmsSet.peakwidth: xcmsSet.peakwidth
xcmsSet.polarity: xcmsSet.polarity
xcmsSet.ppm: xcmsSet.ppm
xcmsSet.prefilter: xcmsSet.prefilter
xcmsSet.profparam: xcmsSet.profparam
xcmsSet.sleep: xcmsSet.sleep
xcmsSet.snthresh: xcmsSet.snthresh
xcmsSet.step: xcmsSet.step
xcmsSet.verbose.columns: xcmsSet.verbose.columns
zero2NA: Convert the value <=0 to NA

Functions

addIdentInfo Man page
addValueNorm<- Man page
autoRemoveOutlier Man page
bootPLSDA Man page
calcAUROC Man page
calcVIP Man page
center<- Man page
checkPvaluePlot Man page
checkQCPlot Man page
cor.network Man page
createModels Man page
dataClean Man page
dir.case<- Man page
dir.ctrl<- Man page
doQCRLSC Man page
featureSelection Man page
filterPeaks Man page
filterQCPeaks Man page
filterQCPeaksByCV Man page
getPeaksTable Man page
group.bw0<- Man page
group.bw<- Man page
group.max<- Man page
group.minfrac<- Man page
group.minsamp<- Man page
group.mzwid0<- Man page
group.mzwid<- Man page
group.sleep<- Man page
hasQC Man page
idres<- Man page
importDataFromMetaboAnalyst Man page
importDataFromQI Man page
importDataFromXCMS Man page
kfold<- Man page
makeDirectory Man page
makeMetaboAnalystInput Man page
metaXpara-class Man page
metaXpipe Man page
metaboliteAnnotation Man page
method<- Man page
missValueImputeMethod<- Man page
missingValueImpute Man page
myCalcAUROC Man page
myPLSDA Man page
ncomp<- Man page
normalize Man page
nperm<- Man page
outdir<- Man page
pathwayAnalysis Man page
peakFinder Man page
peakStat Man page
peaksData<- Man page
permutePLSDA Man page
plotCV Man page
plotCorHeatmap Man page
plotHeatMap Man page
plotIntDistr Man page
plotLoading Man page
plotMissValue Man page
plotNetwork Man page
plotPCA Man page
plotPLSDA Man page
plotPeakBox Man page
plotPeakNumber Man page
plotPeakSN Man page
plotPeakSumDist Man page
plotQC Man page
plotQCRLSC Man page
plotTreeMap Man page
plsDAPara-class Man page
powerAnalyst Man page
preProcess Man page
prefix<- Man page
qcRlscSpan<- Man page
ratioPairs<- Man page
rawPeaks<- Man page
reSetPeaksData Man page
removeSample Man page
retcor.method<- Man page
retcor.plottype<- Man page
retcor.profStep<- Man page
runPLSDA Man page
sampleListFile<- Man page
scale<- Man page
selectBestComponent Man page
t<- Man page
transformation Man page
validation<- Man page
xcmsSet.fitgauss<- Man page
xcmsSet.fwhm<- Man page
xcmsSet.integrate<- Man page
xcmsSet.max<- Man page
xcmsSet.method<- Man page
xcmsSet.mzCenterFun<- Man page
xcmsSet.mzdiff<- Man page
xcmsSet.nSlaves<- Man page
xcmsSet.noise<- Man page
xcmsSet.peakwidth<- Man page
xcmsSet.polarity<- Man page
xcmsSet.ppm<- Man page
xcmsSet.prefilter<- Man page
xcmsSet.profparam<- Man page
xcmsSet.sleep<- Man page
xcmsSet.snthresh<- Man page
xcmsSet.step<- Man page
xcmsSet.verbose.columns<- Man page
xcmsSetObj<- Man page
zero2NA Man page

Files

metaX/DESCRIPTION
metaX/NAMESPACE
metaX/NEWS
metaX/R
metaX/R/MetaboliteIdentify.R
metaX/R/ROC.R
metaX/R/bootPLSDA.R
metaX/R/fselection.R
metaX/R/metaX.R
metaX/R/model.R
metaX/R/network.R
metaX/R/pathwayAnalysis.R
metaX/R/powerAnalysis.R
metaX/R/prep.R
metaX/R/tool.R
metaX/R/zzz.R
metaX/build
metaX/build/vignette.rds
metaX/inst
metaX/inst/doc
metaX/inst/doc/metaX.R
metaX/inst/doc/metaX.Rnw
metaX/inst/doc/metaX.pdf
metaX/inst/extdata
metaX/inst/extdata/MTBLS79.txt
metaX/inst/extdata/MTBLS79_sampleList.txt
metaX/inst/extdata/faahKO_sampleList.txt
metaX/inst/tool
metaX/inst/tool/MetaboliteIdentify.jar
metaX/inst/unitTests
metaX/inst/unitTests/test_hasQC.R
metaX/inst/unitTests/test_metaXpipe.R
metaX/inst/unitTests/test_rfSelection.R
metaX/man
metaX/man/addIdentInfo.Rd
metaX/man/addValueNorm.Rd
metaX/man/autoRemoveOutlier.Rd
metaX/man/bootPLSDA.Rd
metaX/man/calcAUROC.Rd
metaX/man/calcVIP.Rd
metaX/man/center.Rd
metaX/man/checkPvaluePlot.Rd
metaX/man/checkQCPlot.Rd
metaX/man/cor.network.Rd
metaX/man/createModels.Rd
metaX/man/dataClean.Rd
metaX/man/dir.case.Rd
metaX/man/dir.ctrl.Rd
metaX/man/doQCRLSC.Rd
metaX/man/featureSelection.Rd
metaX/man/filterPeaks.Rd
metaX/man/filterQCPeaks.Rd
metaX/man/filterQCPeaksByCV.Rd
metaX/man/getPeaksTable.Rd
metaX/man/group.bw.Rd
metaX/man/group.bw0.Rd
metaX/man/group.max.Rd
metaX/man/group.minfrac.Rd
metaX/man/group.minsamp.Rd
metaX/man/group.mzwid.Rd
metaX/man/group.mzwid0.Rd
metaX/man/group.sleep.Rd
metaX/man/hasQC.Rd
metaX/man/idres.Rd
metaX/man/importDataFromMetaboAnalyst.Rd
metaX/man/importDataFromQI.Rd
metaX/man/importDataFromXCMS.Rd
metaX/man/kfold.Rd
metaX/man/makeDirectory.Rd
metaX/man/makeMetaboAnalystInput.Rd
metaX/man/metaXpara-class.Rd
metaX/man/metaXpipe.Rd
metaX/man/metaboliteAnnotation.Rd
metaX/man/method.Rd
metaX/man/missValueImputeMethod.Rd
metaX/man/missingValueImpute.Rd
metaX/man/myCalcAUROC.Rd
metaX/man/myPLSDA.Rd
metaX/man/ncomp.Rd
metaX/man/normalize.Rd
metaX/man/nperm.Rd
metaX/man/outdir.Rd
metaX/man/pathwayAnalysis.Rd
metaX/man/peakFinder.Rd
metaX/man/peakStat.Rd
metaX/man/peaksData.Rd
metaX/man/permutePLSDA.Rd
metaX/man/plotCV.Rd
metaX/man/plotCorHeatmap.Rd
metaX/man/plotHeatMap.Rd
metaX/man/plotIntDistr.Rd
metaX/man/plotLoading.Rd
metaX/man/plotMissValue.Rd
metaX/man/plotNetwork.Rd
metaX/man/plotPCA.Rd
metaX/man/plotPLSDA.Rd
metaX/man/plotPeakBox.Rd
metaX/man/plotPeakNumber.Rd
metaX/man/plotPeakSN.Rd
metaX/man/plotPeakSumDist.Rd
metaX/man/plotQC.Rd
metaX/man/plotQCRLSC.Rd
metaX/man/plotTreeMap.Rd
metaX/man/plsDAPara-class.Rd
metaX/man/powerAnalyst.Rd
metaX/man/preProcess.Rd
metaX/man/prefix.Rd
metaX/man/qcRlscSpan.Rd
metaX/man/ratioPairs.Rd
metaX/man/rawPeaks.Rd
metaX/man/reSetPeaksData.Rd
metaX/man/removeSample.Rd
metaX/man/retcor.method.Rd
metaX/man/retcor.plottype.Rd
metaX/man/retcor.profStep.Rd
metaX/man/runPLSDA.Rd
metaX/man/sampleListFile.Rd
metaX/man/scale.Rd
metaX/man/selectBestComponent.Rd
metaX/man/t.Rd
metaX/man/transformation.Rd
metaX/man/validation.Rd
metaX/man/xcmsSet.fitgauss.Rd
metaX/man/xcmsSet.fwhm.Rd
metaX/man/xcmsSet.integrate.Rd
metaX/man/xcmsSet.max.Rd
metaX/man/xcmsSet.method.Rd
metaX/man/xcmsSet.mzCenterFun.Rd
metaX/man/xcmsSet.mzdiff.Rd
metaX/man/xcmsSet.nSlaves.Rd
metaX/man/xcmsSet.noise.Rd
metaX/man/xcmsSet.peakwidth.Rd
metaX/man/xcmsSet.polarity.Rd
metaX/man/xcmsSet.ppm.Rd
metaX/man/xcmsSet.prefilter.Rd
metaX/man/xcmsSet.profparam.Rd
metaX/man/xcmsSet.sleep.Rd
metaX/man/xcmsSet.snthresh.Rd
metaX/man/xcmsSet.step.Rd
metaX/man/xcmsSet.verbose.columns.Rd
metaX/man/xcmsSetObj.Rd
metaX/man/zero2NA.Rd
metaX/tests
metaX/tests/runTests.R
metaX/vignettes
metaX/vignettes/metaX.Rnw
metaX/vignettes/metaX.bib
metaX documentation built on Oct. 5, 2016, 4:41 a.m.