metaX: An R package for metabolomic data analysis

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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.

Author
Bo Wen <wenbo@genomics.cn>
Date of publication
None
Maintainer
Bo Wen <wenbo@genomics.cn>
License
LGPL-2
Version
1.4.2
URLs

View on Bioconductor

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

Files in this package

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