An R package for metabolomic data analysis


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Documentation for package ‘metaX’ version 1.0.3

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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