Statistical Analysis of Metabolomic Data


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Documentation for package ‘MAIT’ version 1.12.0

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Biotransformations Biotransformations of the significant data contained in a MAIT object are identified.
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 object
getScoresTable Returns a list with the peak scores, masses, retention time and other information
identifyMetabolites Metabolite identifier
loadings Loadings extractor for either PCA or PLS models
loadings-method Class '"MAIT"'
LSDResults Extractor of the Fisher's LSD tests from a MAIT object
MAIT MAIT
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"'
MAITbuilder MAIT constructor function when using external peak data
metaboliteTable Metabolite table generator
model Model extractor for either PCA or PLS models
model-method Class '"MAIT"'
models Model extractor from a MAIT object
negAdducts Negative adducts table
ovClassifRatioData 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 object
peakAnnotation Spectra constructor and peak annotator
plotBoxplot Prints a png file for each of the significant peak/spectra present in the input
plotHeatmap Builds ten heatmaps with different p-values and clustering distances
plotPCA 2D and 3D PCA scoreplots from a MAIT object
plotPLS 2D and 3D PLS scoreplots from a MAIT object
posAdducts Positive adducts table
pvalues Pvalues extractor from a MAIT object
pvaluesCorrection P-values correction extractor from a MAIT object
rawData Raw data extractor from a MAIT object
resultsPath Retrieves the folder where the results are saved for a MAIT object
sampleProcessing Peak detector of netCDF samples using xcms package
scores Retrieves the scores from a MAIT object
scores-method Class '"MAIT"'
sigPeaksTable Build a table of the information related to the significant features contained in a MAIT object
spectralSigFeatures Extract significant features from a MAIT object
summary-method Class '"MAIT"'
Validation Cross validated classification over the output of the function 'signPeaksAnova' or function 'TStudent2Clases'