Man pages for MAIT
Statistical Analysis of Metabolomic Data
| 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... |
