# Statistical Analysis of Metabolomic Data

## Documentation for package ‘MAIT’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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'