| 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' |