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' |