Package: MAIT 1.41.0

Pol Sola-Santos

MAIT: Statistical Analysis of Metabolomic Data

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.

Authors:Francesc Fernandez-Albert, Rafael Llorach, Cristina Andres-LaCueva, Alexandre Perera

MAIT_1.41.0.tar.gz
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MAIT.pdf |MAIT.html✨
MAIT/json (API)
NEWS

# Install 'MAIT' in R:

install.packages('MAIT', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

Database - Human Metabolome Database
MAIT - MAIT
biotransformationsTable - BiotransformationsTable
negAdducts - Negative adducts table
posAdducts - Positive adducts table

On BioConductor:MAIT-1.41.0(bioc 3.21)MAIT-1.40.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology massspectrometry metabolomics software

4.60 score 20 scripts 367 downloads 16 mentions 41 exports 194 dependencies

Last updated 23 days agofrom:2f8e62b4a0. Checks:OK: 1 NOTE: 4 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 31 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	WARNING	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	WARNING	Oct 31 2024

Exports:Biotransformations classes classifRatioClasses classNum featureID featureInfo featureSigID getScoresTable identifyMetabolites loadings LSDResults MAITbuilder metaboliteTable method model models ovClassifRatioData ovClassifRatioTable parameters pcaLoadings pcaModel pcaScores peakAggregation peakAnnotation plotBoxplot plotHeatmap plotPCA plotPLS plsLoadings plsModel plsScores pvalues pvaluesCorrection rawData resultsPath sampleProcessing scores sigPeaksTable spectralSigFeatures summary Validation

Dependencies:abind affy affyio agricolae AlgDesign AnnotationFilter askpass backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocManager BiocParallel bitops boot bslib cachem CAMERA caret caTools checkmate class cli clock clue cluster codetools colorspace cpp11 crayon crosstalk curl data.table DBI DelayedArray diagram digest doParallel dotCall64 dplyr e1071 evaluate fansi farver fastmap fields fontawesome foreach foreign formatR Formula fs futile.logger futile.options future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 globals glue gower gplots graph gridExtra gtable gtools hardhat highr Hmisc hms htmlTable htmltools htmlwidgets httr igraph impute ipred IRanges isoband iterators jquerylib jsonlite KernSmooth knitr labeling lambda.r later lattice lava lazyeval lifecycle limma listenv lubridate magrittr MALDIquant maps MASS MassSpecWavelet Matrix MatrixGenerics matrixStats memoise MetaboCoreUtils mgcv mime ModelMetrics MsCoreUtils MsExperiment MsFeatures MSnbase MultiAssayExperiment munsell mzID mzR ncdf4 nlme nnet numDeriv openssl parallelly pcaMethods pillar pkgconfig plotly pls plsgenomics plyr preprocessCore prettyunits pROC prodlim progress progressr promises ProtGenerics proxy PSMatch purrr QFeatures R6 rappdirs RBGL RColorBrewer Rcpp recipes reshape2 Rhdf5lib RhpcBLASctl rlang rmarkdown rpart rstudioapi S4Arrays S4Vectors sass scales shape snow spam SparseArray Spectra SQUAREM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange timeDate tinytex tzdb UCSC.utils utf8 vctrs viridis viridisLite vsn withr xcms xfun XML XVector yaml zlibbioc

\maketitleMAIT Vignette

Rendered fromMAIT_Vignette.Rnwusingutils::Sweaveon Oct 31 2024.

Last update: 2017-04-24
Started: 2014-10-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Biotransformations of the significant data contained in a MAIT object are identified.	Biotransformations
biotransformationsTable	biotransformationsTable
Class names extractor from a MAIT object	classes
Class classification ratio extractor from a MAIT object	classifRatioClasses
Sample number extractor for each class from a MAIT object	classNum
Human Metabolome Database	Database
Feature ID extractor from a MAIT object	featureID
Feature Info extractor from a MAIT object	featureInfo
Feature statistically significant ID extractor from a MAIT object	featureSigID
Returns a list with the peak scores, masses, retention time and other information	getScoresTable
Metabolite identifier	identifyMetabolites
Loadings extractor for either PCA or PLS models	loadings
Extractor of the Fisher's LSD tests from a MAIT object	LSDResults
MAIT	MAIT
Class '"MAIT"'	loadings,MAIT-method MAIT-class model,MAIT-method scores,MAIT-method summary,MAIT-method
Class '"MAIT.FeatureData"'	MAIT.FeatureData-class
Class '"MAIT.FeatureInfo"'	MAIT.FeatureInfo-class
Class '"MAIT.Parameters"'	MAIT.Parameters-class
Class '"MAIT.PhenoData"'	MAIT.PhenoData-class
Class '"MAIT.RawData"'	MAIT.RawData-class
Class '"MAIT.Validation"'	MAIT.Validation-class
MAIT constructor function when using external peak data	MAITbuilder
Metabolite table generator	metaboliteTable
Model extractor for either PCA or PLS models	model
Model extractor from a MAIT object	models
Negative adducts table	negAdducts
Overall classification ratio extractor for MAIT objects	ovClassifRatioData
Overall classification table extractor for MAIT objects	ovClassifRatioTable
Extractor of the parameters used in the whole run from a MAIT object	parameters
Spectra constructor and peak annotator	peakAnnotation
Prints a png file for each of the significant peak/spectra present in the input	plotBoxplot
Builds ten heatmaps with different p-values and clustering distances	plotHeatmap
2D and 3D PCA scoreplots from a MAIT object	plotPCA
2D and 3D PLS scoreplots from a MAIT object	plotPLS
Positive adducts table	posAdducts
Pvalues extractor from a MAIT object	pvalues
P-values correction extractor from a MAIT object	pvaluesCorrection
Raw data extractor from a MAIT object	rawData
Retrieves the folder where the results are saved for a MAIT object	resultsPath
Peak detector of netCDF samples using xcms package	sampleProcessing
Retrieves the scores from a MAIT object	scores
Build a table of the information related to the significant features contained in a MAIT object	sigPeaksTable
Extract significant features from a MAIT object	spectralSigFeatures
Cross validated classification over the output of the function 'signPeaksAnova' or function 'TStudent2Clases'	Validation