Package: GARS 1.27.0

Mattia Chiesa

GARS: GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets

Feature selection aims to identify and remove redundant, irrelevant and noisy variables from high-dimensional datasets. Selecting informative features affects the subsequent classification and regression analyses by improving their overall performances. Several methods have been proposed to perform feature selection: most of them relies on univariate statistics, correlation, entropy measurements or the usage of backward/forward regressions. Herein, we propose an efficient, robust and fast method that adopts stochastic optimization approaches for high-dimensional. GARS is an innovative implementation of a genetic algorithm that selects robust features in high-dimensional and challenging datasets.

Authors:Mattia Chiesa <[email protected]>, Luca Piacentini <[email protected]>

GARS_1.27.0.tar.gz
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GARS.pdf |GARS.html
GARS/json (API)
NEWS

# Install 'GARS' in R:
install.packages('GARS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • openjdk– OpenJDK Java runtime, using Hotspot JIT
Datasets:

On BioConductor:GARS-1.27.0(bioc 3.21)GARS-1.26.0(bioc 3.20)

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

classificationfeatureextractionclustering

5.00 score 2 scripts 189 downloads 13 mentions 13 exports 259 dependencies

Last updated 23 days agofrom:d0acef70f1. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winOKNov 19 2024
R-4.5-linuxOKNov 19 2024
R-4.4-winOKNov 19 2024
R-4.4-macOKNov 19 2024
R-4.3-winOKNov 19 2024
R-4.3-macOKNov 19 2024

Exports:AllPopFitScoreGARS_create_rnd_populationGARS_CrossoverGARS_ElitismGARS_FitFunGARS_GAGARS_MutationGARS_PlotFeaturesUsageGARS_PlotFitnessEvolutionGARS_SelectionLastPopMatrixFeatures

Dependencies:abindannotateAnnotationDbiarmaroma.lightaskpassbackportsbase64encbdsmatrixBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelbiomaRtBiostringsbitbit64bitopsblobbootbriobroombslibcachemcallrcarcarDatacaretcaToolscheckmateclasscliclockclustercodacodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkcurlDaMiRseqdata.tableDBIdbplyrDelayedArraydeldirDerivdescDESeq2diagramdiffobjdigestdoBydplyrDTe1071EDASeqedgeRellipseemmeansentropyestimabilityevaluateFactoMineRfansifarverfastmapfilelockflashClustfontawesomeforeachforeignformatRFormulafsFSelectorfutile.loggerfutile.optionsfuturefuture.applygenalggenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggrepelglobalsgluegowergridExtragtablehardhathighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2hwriterigraphineqinterpipredIRangesisobanditeratorsjpegjquerylibjsonliteKEGGRESTKernSmoothkknnknitrlabelinglambda.rlaterlatticelatticeExtralavalazyevalleapslifecyclelimmalistenvlme4locfitlubridatemagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqaMLSeqModelMetricsmodelrmultcompViewmunsellmvtnormnlmenloptrnnetnumDerivopensslpamrparallellypbkrtestpheatmappillarpkgbuildpkgconfigpkgloadplogrplsplsVarSelplyrpngpraisepraznikprettyunitspROCprocessxprodlimprogressprogressrpromisesproxypspurrrpwalignquantregR.methodsS3R.ooR.utilsR6randomForestrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlrecipesreshape2restfulrRhtslibrJavarjsonrlangrmarkdownrpartrprojrootRsamtoolsRSNNSRSQLiterstudioapirtracklayerRWekaRWekajarsS4ArraysS4Vectorssassscalesscatterplot3dshapeShortReadsnowSparseArraySparseMSQUAREMsSeqstatmodstringistringrSummarizedExperimentsurvivalsvasystestthattibbletidyrtidyselecttimechangetimeDatetinytextzdbUCSC.utilsutf8vctrsVennDiagramviridisviridisLitewaldowithrxfunXMLxml2xtableXVectoryamlzlibbioc

GARS: a Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional and challenging datasets

Rendered fromGARS.Rnwusingknitr::knitron Nov 19 2024.

Last update: 2020-04-14
Started: 2018-02-12

Readme and manuals

Help Manual

Help pageTopics
Accessors for the 'AllPop' slot of a GarsSelectedFeatures object.AllPop AllPop,GARS-AllPop AllPop,GarsSelectedFeatures-method
Accessors for the 'FitScore' slot of a GarsSelectedFeatures object.FitScore FitScore,GARS-FitScore FitScore,GarsSelectedFeatures-method
GARS package for a robust feature selection of high-dimensional dataGARS-package GARS
RNA-seq dataset for testing GARSGARS_classes
Create a random chromosomes populationGARS_create_rnd_population
Perform the one-point and the two-point CrossoverGARS_Crossover
RNA-seq dataset for testing GARSGARS_data_norm
Separate chromosome on the basis of the Fitness ScoresGARS_Elitism
RNA-seq dataset for testing GARSGARS_fit_list
This function implements the Fitness Function of GARSGARS_FitFun
RNA-seq dataset for testing GARSGARS_Fitness_score
The wrapper fuction to use GARSGARS_GA
Perform the Mutation stepGARS_Mutation
A bubble chart to assess the usage of each featuresGARS_PlotFeaturesUsage
Plot the maximum fitness scores for each generationGARS_PlotFitnessEvolution
RNA-seq dataset for testing GARSGARS_pop_list
RNA-seq dataset for testing GARSGARS_popul
A GarsSelectedFeatures object for testing GARSGARS_res_GA
Perform the "Roulette Wheel" or the "Tournament" selectionGARS_Selection
The output class 'GarsSelectedFeatures'GarsSelectedFeatures-class
Accessors for the 'LastPop' slot of a GarsSelectedFeatures object.LastPop LastPop,GARS-LastPop LastPop,GarsSelectedFeatures-method
Accessors for the 'MatrixFeatures' slot of a GarsSelectedFeatures object.MatrixFeatures MatrixFeatures,GARS-MatrixFeatures MatrixFeatures,GarsSelectedFeatures-method