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

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.bw<- Man page
group.bw0<- Man page
group.max<- Man page
group.minfrac<- Man page
group.minsamp<- Man page
group.mzwid<- Man page
group.mzwid0<- 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
metaboliteAnnotation Man page
metaXpara-class Man page
metaXpipe Man page
method<- Man page
missingValueImpute Man page
missValueImputeMethod<- 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
peaksData<- Man page
peakStat Man page
permutePLSDA Man page
plotCorHeatmap Man page
plotCV Man page
plotHeatMap Man page
plotIntDistr Man page
plotLoading Man page
plotMissValue Man page
plotNetwork Man page
plotPCA Man page
plotPeakBox Man page
plotPeakNumber Man page
plotPeakSN Man page
plotPeakSumDist Man page
plotPLSDA Man page
plotQC Man page
plotQCRLSC Man page
plotTreeMap Man page
plsDAPara-class Man page
powerAnalyst Man page
prefix<- Man page
preProcess Man page
qcRlscSpan<- Man page
ratioPairs<- Man page
rawPeaks<- Man page
removeSample Man page
reSetPeaksData 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.noise<- Man page
xcmsSet.nSlaves<- Man page
xcmsSetObj<- 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
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

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