Man pages for MAIT
Statistical Analysis of Metabolomic Data

annotateBiotransfSingle Biotransformation Annotator
BiotransformationsBiotransformations of the significant data contained in a...
biotransformationsTablebiotransformationsTable
classesClass names extractor from a MAIT object
classifRatioClassesClass classification ratio extractor from a MAIT object
classNumSample number extractor for each class from a MAIT object
DatabaseHuman Metabolome Database
featureIDFeature ID extractor from a MAIT object
featureInfoFeature Info extractor from a MAIT object
featureSigIDFeature statistically significant ID extractor from a MAIT...
FisherLSDPerforms Fisher's LSD tests on the provided data
getScoresTableReturns a list with the peak scores, masses, retention time...
identifyMetabolitesMetabolite identifier
inBetweenChecks if a peak mass value is in a certain mass allowance...
loadingsLoadings extractor for either PCA or PLS models
LSDResultsExtractor of the Fisher's LSD tests from a MAIT object
MAITbuilderMAIT constructor function when using external peak data
MAIT-classClass '"MAIT"'
MAIT_dataSetMAIT
MAIT.FeatureData-classClass '"MAIT.FeatureData"'
MAIT.FeatureInfo-classClass '"MAIT.FeatureInfo"'
MAIT.Parameters-classClass '"MAIT.Parameters"'
MAIT.PhenoData-classClass '"MAIT.PhenoData"'
MAIT.RawData-classClass '"MAIT.RawData"'
MAIT.Validation-classClass '"MAIT.Validation"'
metaboliteTableMetabolite table generator
methodPeak Aggregation Method Used
modelModel extractor for either PCA or PLS models
modelsModel extractor from a MAIT object
negAdductsNegative adducts table
ovClassifRatioOverall classification ratio extractor for MAIT objects
ovClassifRatioTableOverall classification table extractor for MAIT objects
parametersExtractor of the parameters used in the whole run from a MAIT...
pcaLoadingsLoadings extractor for the PCA model
pcaModelModel extractor for either PCA
PCAplot3d3D PCA scoreplots
pcaScoresScores extractor for the PCA model
peakAggregationPerforms a peak aggregation procedure to the rawData of a...
peakAnnotationSpectra constructor and peak annotator
plotBoxplotPrints a png file for each of the significant peak/spectra...
plotHeatmapBuilds ten heatmaps with different p-values and clustering...
plotPCA2D and 3D PCA scoreplots from a MAIT object
plotPLS2D and 3D PLS scoreplots from a MAIT object
PLSDAApplies PLSDA to the provided data
plsLoadingsLoadings extractor for the PLS model
plsModelModel extractor for either PLS
plsScoresScores extractor for the PLS model
posAdductsPositive adducts table
projectChange the basis of the MAIT data
pvaluesPvalues extractor from a MAIT object
pvaluesCorrectionP-values correction extractor from a MAIT object
rawDataRaw data extractor from a MAIT object
removeOnePeakSpectraRemoves those spectra having just one peak
resultsPathRetrieves the folder where the results are saved for a MAIT...
retrieveSpectrumExtractor of the mass peaks corresponding to a certain...
sampleProcessingPeak detector of netCDF samples using xcms package
scoresRetrieves the scores from a MAIT object
SearchCandPeak search function into a database
selectKLooks for the optimum number of nearest neighbours to be...
selectPLScompLooks for the optimum number of components to be considered...
sigPeaksTableBuild a table of the information related to the significant...
spectralAnovaExtract significant features from a MAIT object
spectralFUNExtract significant features from a MAIT object using a...
spectralKruskalExtract significant features from a MAIT object
spectralSigFeaturesExtract significant features from a MAIT object
spectralTStudentExtract significant features from a MAIT object for two...
spectralWelchExtract significant features from a MAIT object
spectralWilcoxExtract significant features from a MAIT object
successRatioExtracts the success ratio of a truth table
ValidationCross validated classification over the output of the...
writeExcelTableWrites a csv table
writeParameterTableWrites a csv table containing the parameters launched in the...
MAIT documentation built on May 31, 2017, 11:38 a.m.