MAIT: Statistical Analysis of Metabolomic Data

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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.

Author
Francesc Fernandez-Albert, Rafael Llorach, Cristina Andres-LaCueva, Alexandre Perera
Date of publication
None
Maintainer
Francesc Fernandez-Albert <francesc.fernandez.albert@upc.edu>
License
GPL-2
Version
1.8.0

View on Bioconductor

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...

Files in this package

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