MAIT: Statistical Analysis of Metabolomic Data

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.

AuthorFrancesc Fernandez-Albert, Rafael Llorach, Cristina Andres-LaCueva, Alexandre Perera
Date of publicationNone
MaintainerFrancesc Fernandez-Albert <francesc.fernandez.albert@upc.edu>
LicenseGPL-2
Version1.8.0

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.