metaX: An R package for metabolomic data analysis

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.

AuthorBo Wen <wenbo@genomics.cn>
Date of publicationNone
MaintainerBo Wen <wenbo@genomics.cn>
LicenseLGPL-2
Version1.4.2
http://wenbostar.github.io/metaX/

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

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