# An R package for metabolomic data analysis

## Documentation for package ‘metaX’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D F G H I K M N O P Q R S T V X Z

## -- A --

addIdentInfo | Add identification result into metaXpara object
addIdentInfo-method | Add identification result into metaXpara object
addValueNorm<- | addValueNorm
addValueNorm<--method | An S4 class to represent the parameters and data for data processing
autoRemoveOutlier | Automatically detect outlier samples
autoRemoveOutlier-method | Automatically detect outlier samples

## -- B --

bootPLSDA | Fit predictive models for PLS-DA

## -- C --

calcAUROC | Classical univariate ROC analysis
calcAUROC-method | Classical univariate ROC analysis
calcVIP | Calculate the VIP for PLS-DA
calcVIP-method | Calculate the VIP for PLS-DA
center<- | center
center<--method | An S4 class to represent the parameters for PLS-DA analysis
cor.network | Correlation network analysis
createModels | Create predictive models

## -- D --

dataClean | dataClean
dataClean-method | dataClean
dir.case<- | dir.case
dir.case<--method | An S4 class to represent the parameters and data for data processing
dir.ctrl<- | dir.ctrl
dir.ctrl<--method | An S4 class to represent the parameters and data for data processing
doQCRLSC | Using the QC samples to do the quality control-robust spline signal correction
doQCRLSC-method | Using the QC samples to do the quality control-robust spline signal correction

## -- F --

featureSelection | Feature selection and modeling
filterPeaks | filterPeaks
filterPeaks-method | filterPeaks
filterQCPeaks | filterQCPeaks
filterQCPeaks-method | filterQCPeaks
filterQCPeaksByCV | Filter peaks according to the RSD of peaks in QC samples
filterQCPeaksByCV-method | Filter peaks according to the RSD of peaks in QC samples

## -- G --

getPeaksTable | Get a data.frame which contained the peaksData in metaXpara
getPeaksTable-method | Get a data.frame which contained the peaksData in metaXpara
group.bw0<- | group.bw0
group.bw0<--method | An S4 class to represent the parameters and data for data processing
group.bw<- | group.bw
group.bw<--method | An S4 class to represent the parameters and data for data processing
group.max<- | group.max
group.max<--method | An S4 class to represent the parameters and data for data processing
group.minfrac<- | group.minfrac
group.minfrac<--method | An S4 class to represent the parameters and data for data processing
group.minsamp<- | group.minsamp
group.minsamp<--method | An S4 class to represent the parameters and data for data processing
group.mzwid0<- | group.mzwid0
group.mzwid0<--method | An S4 class to represent the parameters and data for data processing
group.mzwid<- | group.mzwid
group.mzwid<--method | An S4 class to represent the parameters and data for data processing
group.sleep<- | group.sleep
group.sleep<--method | An S4 class to represent the parameters and data for data processing

## -- H --

hasQC | Judge whether the data has QC samples
hasQC-method | Judge whether the data has QC samples

## -- I --

idres<- | idres
idres<--method | An S4 class to represent the parameters and data for data processing

## -- K --

kfold<- | kfold
kfold<--method | An S4 class to represent the parameters for PLS-DA analysis

## -- M --

makeDirectory | Create directory
makeDirectory-method | Create directory
makeMetaboAnalystInput | Export a csv file which can be used for MetaboAnalyst
makeMetaboAnalystInput-method | 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 processing
metaXpipe | metaXpipe
metaXpipe-method | metaXpipe
method<- | method
method<--method | An S4 class to represent the parameters for PLS-DA analysis
missingValueImpute | Missing value imputation
missingValueImpute-method | Missing value imputation
missValueImputeMethod<- | missValueImputeMethod
missValueImputeMethod<--method | An S4 class to represent the parameters and data for data processing
myCalcAUROC | Classical univariate ROC analysis
myPLSDA | Perform PLS-DA analysis
myPLSDA-method | Perform PLS-DA analysis

## -- N --

ncomp<- | ncomp
ncomp<--method | An S4 class to represent the parameters for PLS-DA analysis
normalize | Normalisation of peak intensity
normalize-method | Normalisation of peak intensity
nperm<- | nperm
nperm<--method | An S4 class to represent the parameters for PLS-DA analysis

## -- O --

outdir<- | outdir
outdir<--method | An S4 class to represent the parameters and data for data processing

## -- P --

pathwayAnalysis | Pathway analysis
peakFinder | Peak detection by using XCMS package
peakFinder-method | Peak detection by using XCMS package
peaksData<- | peaksData
peaksData<--method | An S4 class to represent the parameters and data for data processing
peakStat | Do the univariate and multivariate statistical analysis
peakStat-method | Do the univariate and multivariate statistical analysis
permutePLSDA | permutePLSDA
plotCorHeatmap | Plot correlation heatmap
plotCV | Plot the CV distribution of peaks in each group
plotCV-method | Plot the CV distribution of peaks in each group
plotHeatMap | Plot heatmap
plotHeatMap-method | Plot heatmap
plotIntDistr | Plot the distribution of the peaks intensity
plotIntDistr-method | Plot the distribution of the peaks intensity
plotMissValue | Plot missing value distribution
plotMissValue-method | Plot missing value distribution
plotNetwork | Plot correlation network map
plotPCA | Plot PCA figure
plotPCA-method | Plot PCA figure
plotPeakBox | Plot boxplot for each feature
plotPeakBox-method | Plot boxplot for each feature
plotPeakNumber | Plot the distribution of the peaks number
plotPeakNumber-method | Plot the distribution of the peaks number
plotPeakSN | Plot the distribution of the peaks S/N
plotPeakSN-method | Plot the distribution of the peaks S/N
plotPeakSumDist | Plot the total peak intensity distribution
plotPeakSumDist-method | Plot the total peak intensity distribution
plotPLSDA | Plot PLS-DA figure
plotPLSDA-method | Plot PLS-DA figure
plotQC | Plot the correlation change of the QC samples.
plotQC-method | Plot the correlation change of the QC samples.
plotQCRLSC | Plot figures for QC-RLSC
plotQCRLSC-method | Plot figures for QC-RLSC
plotTreeMap | Plot Phylogenies for samples
plotTreeMap-method | Plot Phylogenies for samples
plsDAPara-class | An S4 class to represent the parameters for PLS-DA analysis
powerAnalyst | Power Analysis
prefix<- | prefix
prefix<--method | An S4 class to represent the parameters and data for data processing
preProcess | Pre-Processing

## -- Q --

qcRlscSpan<- | qcRlscSpan
qcRlscSpan<--method | An S4 class to represent the parameters and data for data processing

## -- R --

ratioPairs<- | ratioPairs
ratioPairs<--method | An S4 class to represent the parameters and data for data processing
rawPeaks<- | rawPeaks
rawPeaks<--method | An S4 class to represent the parameters and data for data processing
removeSample | Remove samples from the metaXpara object
removeSample-method | Remove samples from the metaXpara object
reSetPeaksData | reSetPeaksData
reSetPeaksData-method | reSetPeaksData
retcor.method<- | retcor.method
retcor.method<--method | An S4 class to represent the parameters and data for data processing
retcor.plottype<- | retcor.plottype
retcor.plottype<--method | An S4 class to represent the parameters and data for data processing
retcor.profStep<- | retcor.profStep
retcor.profStep<--method | An S4 class to represent the parameters and data for data processing
runPLSDA | runPLSDA

## -- S --

sampleListFile<- | sampleListFile
sampleListFile<--method | An S4 class to represent the parameters and data for data processing
scale<- | scale
scale<--method | An S4 class to represent the parameters for PLS-DA analysis
selectBestComponent | Select the best component for PLS-DA

## -- T --

t<- | t
t<--method | An S4 class to represent the parameters for PLS-DA analysis
transformation | Data transformation

## -- V --

validation<- | validation
validation<--method | An S4 class to represent the parameters for PLS-DA analysis

## -- X --

xcmsSet.fitgauss<- | xcmsSet.fitgauss
xcmsSet.fitgauss<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.fwhm<- | xcmsSet.fwhm
xcmsSet.fwhm<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.integrate<- | xcmsSet.integrate
xcmsSet.integrate<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.max<- | xcmsSet.max
xcmsSet.max<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.method<- | xcmsSet.method
xcmsSet.method<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.mzCenterFun<- | xcmsSet.mzCenterFun
xcmsSet.mzCenterFun<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.mzdiff<- | xcmsSet.mzdiff
xcmsSet.mzdiff<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.noise<- | xcmsSet.noise
xcmsSet.noise<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.nSlaves<- | xcmsSet.nSlaves
xcmsSet.nSlaves<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.peakwidth<- | xcmsSet.peakwidth
xcmsSet.peakwidth<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.polarity<- | xcmsSet.polarity
xcmsSet.polarity<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.ppm<- | xcmsSet.ppm
xcmsSet.ppm<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.prefilter<- | xcmsSet.prefilter
xcmsSet.prefilter<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.profparam<- | xcmsSet.profparam
xcmsSet.profparam<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.sleep<- | xcmsSet.sleep
xcmsSet.sleep<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.snthresh<- | xcmsSet.snthresh
xcmsSet.snthresh<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.step<- | xcmsSet.step
xcmsSet.step<--method | An S4 class to represent the parameters and data for data processing
xcmsSet.verbose.columns<- | xcmsSet.verbose.columns
xcmsSet.verbose.columns<--method | An S4 class to represent the parameters and data for data processing
xcmsSetObj<- | xcmsSetObj
xcmsSetObj<--method | An S4 class to represent the parameters and data for data processing

## -- Z --

zero2NA | Convert the value <=0 to NA
zero2NA-method | Convert the value <=0 to NA