MAIT: Statistical Analysis of Metabolomic Data
Version 1.9.0

The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.

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AuthorFrancesc Fernandez-Albert, Rafael Llorach, Cristina Andres-LaCueva, Alexandre Perera
Bioconductor views MassSpectrometry Metabolomics Software
Date of publicationNone
MaintainerFrancesc Fernandez-Albert <francesc.fernandez.albert@upc.edu>
LicenseGPL-2
Version1.9.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MAIT")

Man pages

annotateBiotransf: Single Biotransformation Annotator
Biotransformations: Biotransformations of the significant data contained in a...
biotransformationsTable: biotransformationsTable
classes: Class names extractor from a MAIT object
classifRatioClasses: Class classification ratio extractor from a MAIT object
classNum: Sample number extractor for each class from a MAIT object
Database: Human Metabolome Database
featureID: Feature ID extractor from a MAIT object
featureInfo: Feature Info extractor from a MAIT object
featureSigID: Feature statistically significant ID extractor from a MAIT...
FisherLSD: Performs Fisher's LSD tests on the provided data
getScoresTable: Returns a list with the peak scores, masses, retention time...
identifyMetabolites: Metabolite identifier
inBetween: Checks if a peak mass value is in a certain mass allowance...
loadings: Loadings extractor for either PCA or PLS models
LSDResults: Extractor of the Fisher's LSD tests from a MAIT object
MAITbuilder: MAIT constructor function when using external peak data
MAIT-class: Class '"MAIT"'
MAIT_dataSet: MAIT
MAIT.FeatureData-class: Class '"MAIT.FeatureData"'
MAIT.FeatureInfo-class: Class '"MAIT.FeatureInfo"'
MAIT.Parameters-class: Class '"MAIT.Parameters"'
MAIT.PhenoData-class: Class '"MAIT.PhenoData"'
MAIT.RawData-class: Class '"MAIT.RawData"'
MAIT.Validation-class: Class '"MAIT.Validation"'
metaboliteTable: Metabolite table generator
method: Peak Aggregation Method Used
model: Model extractor for either PCA or PLS models
models: Model extractor from a MAIT object
negAdducts: Negative adducts table
ovClassifRatio: Overall classification ratio extractor for MAIT objects
ovClassifRatioTable: Overall classification table extractor for MAIT objects
parameters: Extractor of the parameters used in the whole run from a MAIT...
pcaLoadings: Loadings extractor for the PCA model
pcaModel: Model extractor for either PCA
PCAplot3d: 3D PCA scoreplots
pcaScores: Scores extractor for the PCA model
peakAggregation: Performs a peak aggregation procedure to the rawData of a...
peakAnnotation: Spectra constructor and peak annotator
plotBoxplot: Prints a png file for each of the significant peak/spectra...
plotHeatmap: Builds ten heatmaps with different p-values and clustering...
plotPCA: 2D and 3D PCA scoreplots from a MAIT object
plotPLS: 2D and 3D PLS scoreplots from a MAIT object
PLSDA: Applies PLSDA to the provided data
plsLoadings: Loadings extractor for the PLS model
plsModel: Model extractor for either PLS
plsScores: Scores extractor for the PLS model
posAdducts: Positive adducts table
project: Change the basis of the MAIT data
pvalues: Pvalues extractor from a MAIT object
pvaluesCorrection: P-values correction extractor from a MAIT object
rawData: Raw data extractor from a MAIT object
removeOnePeakSpectra: Removes those spectra having just one peak
resultsPath: Retrieves the folder where the results are saved for a MAIT...
retrieveSpectrum: Extractor of the mass peaks corresponding to a certain...
sampleProcessing: Peak detector of netCDF samples using xcms package
scores: Retrieves the scores from a MAIT object
SearchCand: Peak search function into a database
selectK: Looks for the optimum number of nearest neighbours to be...
selectPLScomp: Looks for the optimum number of components to be considered...
sigPeaksTable: Build a table of the information related to the significant...
spectralAnova: Extract significant features from a MAIT object
spectralFUN: Extract significant features from a MAIT object using a...
spectralKruskal: Extract significant features from a MAIT object
spectralSigFeatures: Extract significant features from a MAIT object
spectralTStudent: Extract significant features from a MAIT object for two...
spectralWelch: Extract significant features from a MAIT object
spectralWilcox: Extract significant features from a MAIT object
successRatio: Extracts the success ratio of a truth table
Validation: Cross validated classification over the output of the...
writeExcelTable: Writes a csv table
writeParameterTable: Writes a csv table containing the parameters launched in the...

Functions

Biotransformations Man page Source code
Database Man page
FisherLSD Man page Source code
LSDResults Man page Source code
MAIT Man page
MAIT-class Man page
MAIT.FeatureData-class Man page
MAIT.FeatureInfo-class Man page
MAIT.Parameters-class Man page
MAIT.PhenoData-class Man page
MAIT.RawData-class Man page
MAIT.Validation-class Man page
MAITbuilder Man page Source code
PCAplot3d Man page Source code
PLSDA Man page Source code
SearchCand Man page Source code
Validation Man page Source code
annotAdduct Source code
annotateBiotransf Man page Source code
biotransformationsTable Man page
classNum Man page Source code
classes Man page Source code
classifRatioClasses Man page Source code
computeSpectra Source code
featureID Man page Source code
featureInfo Man page Source code
featureSigID Man page Source code
getScoresTable Man page Source code
identifyMetabolites Man page Source code
inBetween Man page Source code
loadings Man page
loadings,MAIT-method Man page
metaboliteTable Man page Source code
method Man page Source code
model Man page
model,MAIT-method Man page
models Man page Source code
negAdducts Man page
ovClassifRatioData Man page Source code
ovClassifRatioTable Man page Source code
parameters Man page Source code
pcaLoadings Man page Source code
pcaModel Man page Source code
pcaScores Man page Source code
peakAggregation Man page Source code
peakAnnotation Man page Source code
plotBoxplot Man page Source code
plotHeatmap Man page Source code
plotPCA Man page Source code
plotPLS Man page Source code
plsLoadings Man page Source code
plsModel Man page Source code
plsScores Man page Source code
posAdducts Man page
project Man page Source code
pvalues Man page Source code
pvaluesCorrection Man page Source code
rawData Man page Source code
removeOnePeakSpectra Man page Source code
resultsPath Man page Source code
retrieveSpectrum Man page Source code
sampleProcessing Man page Source code
scores Man page
scores,MAIT-method Man page
selectK Man page Source code
selectPLScomp Man page Source code
sigPeaksTable Man page Source code
spectralAnova Man page Source code
spectralFUN Man page Source code
spectralKruskal Man page Source code
spectralSigFeatures Man page Source code
spectralTStudent Man page Source code
spectralWelch Man page Source code
spectralWilcox Man page Source code
spectrumAnnotation Source code
successRatio Man page Source code
summary,MAIT-method Man page
writeExcelTable Man page Source code
writeParameterTable Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/Biotransformations.R
R/FisherLSD.R
R/LSDResults.R
R/MAITbuilder.R
R/PLSDA.R
R/SearchCand.R
R/Validation.R
R/classNum.R
R/classes.R
R/classifRatioClasses.R
R/computeSpectra.R
R/featureID.R
R/featureInfo.R
R/featureSigID.R
R/getPeaklist-methods.R
R/getScoresTable.R
R/identifyMetabolites.R
R/loadings-methods.R
R/metaboliteTable.R
R/method.R
R/model-methods.R
R/models.R
R/ovClassifRatioData.R
R/ovClassifRatioTable.R
R/parameters.R
R/pcaLoadings.R
R/pcaModel.R
R/pcaScores.R
R/peakAggregation.R
R/peakAnnotation.R
R/plotBoxplot.R
R/plotHeatmap.R
R/plotPCA.R
R/plotPLS.R
R/plsLoadings.R
R/plsModel.R
R/plsScores.R
R/project.R
R/pvalues.R
R/pvaluesCorrection.R
R/rawData.R
R/removeOnePeakSpectra.R
R/resultsPath.R
R/sampleProcessing.R
R/scores-methods.R
R/selectK.R
R/selectPLScomp.R
R/show-methods.R
R/sigPeaksTable.R
R/spectralAnova.R
R/spectralFUN.R
R/spectralKruskal.R
R/spectralSigFeatures.R
R/spectralTStudent.R
R/spectralWelch.R
R/spectralWilcox.R
R/successRatio.R
R/summary-methods.R
R/writeExcelTable.R
R/writeParameterTable.R
build
build/vignette.rds
data
data/MAIT_sample.RData
data/MAITtables.RData
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/MAIT_Vignette.R
inst/doc/MAIT_Vignette.Rnw
inst/doc/MAIT_Vignette.pdf
man
man/Biotransformations.Rd
man/Database.Rd
man/FisherLSD.Rd
man/LSDResults.Rd
man/MAIT-class.Rd
man/MAIT.FeatureData-class.Rd
man/MAIT.FeatureInfo-class.Rd
man/MAIT.Parameters-class.Rd
man/MAIT.PhenoData-class.Rd
man/MAIT.RawData-class.Rd
man/MAIT.Validation-class.Rd
man/MAIT_dataSet.Rd
man/MAITbuilder.Rd
man/PCAplot3d.Rd
man/PLSDA.Rd
man/SearchCand.Rd
man/Validation.Rd
man/annotateBiotransf.Rd
man/biotransformationsTable.Rd
man/classNum.Rd
man/classes.Rd
man/classifRatioClasses.Rd
man/featureID.Rd
man/featureInfo.Rd
man/featureSigID.Rd
man/getScoresTable.Rd
man/identifyMetabolites.Rd
man/inBetween.Rd
man/loadings.Rd
man/metaboliteTable.Rd
man/method.Rd
man/model.Rd
man/models.Rd
man/negAdducts.Rd
man/ovClassifRatio.Rd
man/ovClassifRatioTable.Rd
man/parameters.Rd
man/pcaLoadings.Rd
man/pcaModel.Rd
man/pcaScores.Rd
man/peakAggregation.Rd
man/peakAnnotation.Rd
man/plotBoxplot.Rd
man/plotHeatmap.Rd
man/plotPCA.Rd
man/plotPLS.Rd
man/plsLoadings.Rd
man/plsModel.Rd
man/plsScores.Rd
man/posAdducts.Rd
man/project.Rd
man/pvalues.Rd
man/pvaluesCorrection.Rd
man/rawData.Rd
man/removeOnePeakSpectra.Rd
man/resultsPath.Rd
man/retrieveSpectrum.Rd
man/sampleProcessing.Rd
man/scores.Rd
man/selectK.Rd
man/selectPLScomp.Rd
man/sigPeaksTable.Rd
man/spectralAnova.Rd
man/spectralFUN.Rd
man/spectralKruskal.Rd
man/spectralSigFeatures.Rd
man/spectralTStudent.Rd
man/spectralWelch.Rd
man/spectralWilcox.Rd
man/successRatio.Rd
man/writeExcelTable.Rd
man/writeParameterTable.Rd
vignettes
vignettes/MAIT_Vignette.Rnw
vignettes/MAIT_objectAnn.RData
vignettes/MAIT_workflow.pdf
vignettes/framed.sty
vignettes/sampleTree.png
MAIT documentation built on May 20, 2017, 9:45 p.m.