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MAIT (version 1.6.0)

Statistical Analysis of Metabolomic Data

Description

The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.

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Version

Version

1.6.0

License

GPL-2

Maintainer

Francesc FernandezAlbert

Last Published

February 15th, 2017

Functions in MAIT (1.6.0)

Biotransformations

Biotransformations of the significant data contained in a MAIT object are identified.

Feature Info extractor from a MAIT object

Peak Aggregation Method Used

Performs Fisher's LSD tests on the provided data

Positive adducts table

Change the basis of the MAIT data

2D and 3D PLS scoreplots from a MAIT object

3D PCA scoreplots

Prints a png file for each of the significant peak/spectra present in the input

removeOnePeakSpectra

Removes those spectra having just one peak

Scores extractor for the PLS model

Human Metabolome Database

Extracts the success ratio of a truth table

Extract significant features from a MAIT object

Model extractor for either PLS

biotransformationsTable

biotransformationsTable

Model extractor for either PCA

spectralSigFeatures

Extract significant features from a MAIT object

sampleProcessing

Peak detector of netCDF samples using xcms package

Feature statistically significant ID extractor from a MAIT object

metaboliteTable

Metabolite table generator

classifRatioClasses

Class classification ratio extractor from a MAIT object

identifyMetabolites

Metabolite identifier

Class names extractor from a MAIT object

Spectra constructor and peak annotator

retrieveSpectrum

Extractor of the mass peaks corresponding to a certain spectrum

annotateBiotransf

Single Biotransformation Annotator

spectralTStudent

Extract significant features from a MAIT object for two classes

writeParameterTable

Writes a csv table containing the parameters launched in the MAIT analysis

Returns a list with the peak scores, masses, retention time and other information

ovClassifRatioTable

Overall classification table extractor for MAIT objects

Model extractor from a MAIT object

pvaluesCorrection

P-values correction extractor from a MAIT object

spectralKruskal

Extract significant features from a MAIT object

Looks for the optimum number of nearest neighbours to be considered for the KNN

Extract significant features from a MAIT object

Build a table of the information related to the significant features contained in a MAIT object

MAIT.Parameters-class

Class "MAIT.Parameters"

MAIT.RawData-class

Class "MAIT.RawData"

Loadings extractor for the PCA model

Extract significant features from a MAIT object using a user-defined test

MAIT constructor function when using external peak data

Applies PLSDA to the provided data

Scores extractor for the PCA model

Peak search function into a database

Builds ten heatmaps with different p-values and clustering distances

Retrieves the folder where the results are saved for a MAIT object

Extract significant features from a MAIT object

Extractor of the parameters used in the whole run from a MAIT object

Raw data extractor from a MAIT object

writeExcelTable

Writes a csv table

Feature ID extractor from a MAIT object

Negative adducts table

ovClassifRatioData

Overall classification ratio extractor for MAIT objects

peakAggregation

Performs a peak aggregation procedure to the rawData of a MAIT object

2D and 3D PCA scoreplots from a MAIT object

MAIT.FeatureInfo-class

Class "MAIT.FeatureInfo"

MAIT.PhenoData-class

Class "MAIT.PhenoData"

Cross validated classification over the output of the function signPeaksAnova or function TStudent2Clases

Sample number extractor for each class from a MAIT object

Looks for the optimum number of components to be considered for the PLSDA

MAIT.FeatureData-class

Class "MAIT.FeatureData"

Retrieves the scores from a MAIT object

MAIT.Validation-class

Class "MAIT.Validation"

Extractor of the Fisher's LSD tests from a MAIT object

Checks if a peak mass value is in a certain mass allowance window.

Loadings extractor for either PCA or PLS models

Model extractor for either PCA or PLS models

Pvalues extractor from a MAIT object

Loadings extractor for the PLS model