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 <firstname.lastname@example.org>|
annotateBiotransf: Single Biotransformation Annotator
Biotransformations: Biotransformations of the significant data contained in a...
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.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...