Package: globaltest 5.61.0
Jelle Goeman
globaltest: Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing
The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.
Authors:
globaltest_5.61.0.tar.gz
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globaltest.pdf |globaltest.html✨
globaltest/json (API)
| # Install 'globaltest' in R: |
| install.packages('globaltest', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:globaltest-5.61.0(bioc 3.21)globaltest-5.60.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
microarrayonechannelbioinformaticsdifferentialexpressiongopathways
Last updated 23 days agofrom:d81273852b. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 20 2024 |
| R-4.5-win | NOTE | Nov 20 2024 |
| R-4.5-linux | NOTE | Nov 20 2024 |
| R-4.4-win | NOTE | Nov 20 2024 |
| R-4.4-mac | NOTE | Nov 20 2024 |
| R-4.3-win | OK | Nov 20 2024 |
| R-4.3-mac | OK | Nov 20 2024 |
Exports:aliasalias<-bbasebtensorcoefficientscombinecomparativecovariatesdrawextractfeaturesfindFocusfitted.valuesfocusLevelgtgt.optionsgtBroadgtConceptgtGOgtKEGGgtKSgtLIgtPShistinheritanceleafNodesmlogitmodel.matrixp.adjustp.valuereparamZresidualsresultreweighZshowsizesortstermssubjectssubsetssummaryweightsz.score
Dependencies:annotateAnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDatagluehttrIRangesjsonliteKEGGRESTlatticelifecycleMatrixmemoisemimeopensslpkgconfigplogrpngR6rlangRSQLiteS4VectorssurvivalsysUCSC.utilsvctrsXMLxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Comparative proportions for the Global Test | comparative |
| Global Test diagnostic plots | covariates diagnostics features subjects |
| Global Test | globaltest gt |
| Gene set testing of gene set databases using Global Test | gtBroad gtConcept gtGO gtKEGG gtKEGGREST |
| Goodness of fit testing in regression models using Global Test | bbase btensor gtKS gtLI gtPS reparamZ reweighZ sterms |
| Class "gt.object" for storing the result of the function gt | alias,gt.object-method alias<- alias<-,gt.object-method extract extract,gt.object-method gt.object gt.object-class hist,gt.object-method length,gt.object-method model.matrix,gt.object-method names,gt.object-method names<-,gt.object-method p.adjust,gt.object-method p.value p.value,gt.object-method result result,gt.object-method show,gt.object-method size size,gt.object-method sort,gt.object-method sterms,gt.object-method subsets subsets,gt.object-method summary,gt.object-method weights,gt.object-method z.score z.score,gt.object-method [,gt.object,ANY,ANY,ANY-method [,gt.object-method [[,gt.object-method |
| Options for globaltest package | gt.options |
| Multinomial Logistic Regression | coefficients,mlogit-method fitted.values,mlogit-method mlogit mlogit-class residuals,mlogit-method show,mlogit-method summary,mlogit-method |
| Multiple testing correction for the Global Test | draw findFocus focusLevel inheritance leafNodes |
