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...

Functions

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

Files

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

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