Package: Category 2.73.0
Bioconductor Package Maintainer
Category: Category Analysis
A collection of tools for performing category (gene set enrichment) analysis.
Authors:
Category_2.73.0.tar.gz
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Category.pdf |Category.html✨
Category/json (API)
NEWS
| # Install 'Category' in R: |
| install.packages('Category', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:Category-2.73.0(bioc 3.21)Category-2.72.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
annotationgopathwaysgenesetenrichment
Last updated 2 months agofrom:1ae31f4d55. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Nov 29 2024 |
| R-4.3-mac | NOTE | Nov 29 2024 |
Exports:.doHyperGTestallGeneIdsannotationannotation<-applyByCategorycateGOrycategoryNamecategoryToEntrezBuildercb_childrencb_contingencycb_parse_band_Hscb_parse_band_Mmcb_sigBandscb_testchildrenOfChrBandTreeFromGraphchrGraphconditionalconditional<-DatPkgFactorydescriptioneffectSizeexampleLevelsexpectedCountsfindAMstatsgeneCountsgeneIdsgeneIds<-geneIdsByCategorygeneIdUniversegeneMappedCountgetPathNamesGO2AllProbesGSEAGOHyperGParamsGSEAKEGGHyperGParamsgseattpermhtmlReporthyperghyperGTestID2EntrezIDID2GOID2KEGGinitializeKEGG2AllProbeslevel2nodeslgeneIdslinearMTestmakeChrBandGraphmakeChrBandGSCmakeChrBandInciMatmakeEBcontrmakeValidParamsMAPAmatNewChrBandTreeOBOCollectionDatPkgOBOHyperGParamsoddsRatiosontologyontology<-organismparentOfprobes2MAPprobes2PathpvalueCutoffpvalueCutoff<-pvaluesshowsigCategoriessummarytestDirectiontestDirection<-testNametreeLevelsttpermuniverseBuilderuniverseCountsuniverseGeneIdsuniverseMappedCount
Dependencies:annotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenefiltergenericsGenomeInfoDbGenomeInfoDbDatagluegraphGSEABasehttrIRangesjsonliteKEGGRESTlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RBGLrlangRSQLiteS4VectorssurvivalsysUCSC.utilsvctrsXMLxtableXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Apply a function to a vector of statistics, by category | applyByCategory |
| Construct a category membership matrix from a list of gene identifiers and their annotated GO categories. | cateGOry |
| Defunct Functions in Package 'Category' | Category-defunct cb_parse_band_hsa chrBandInciMat condGeneIdUniverse geneGoHyperGeoTest geneKeggHyperGeoTest isConditional |
| Return a list mapping category ids to Entrez Gene ids | categoryToEntrezBuilder categoryToEntrezBuilder,GOHyperGParams-method categoryToEntrezBuilder,KEGGHyperGParams-method categoryToEntrezBuilder,OBOHyperGParams-method categoryToEntrezBuilder,PFAMHyperGParams-method |
| Create and Test Contingency Tables of Chromosome Band Annotations | cb_children cb_contingency cb_sigBands |
| Parse Homo Sapiens Chromosome Band Annotations | cb_parse_band_Hs |
| Parse Mus Musculus Chromosome Band Annotations | cb_parse_band_Mm |
| Chromosome Band Tree-Based Hypothesis Testing | cb_test |
| Class "ChrBandTree" | allGeneIds allGeneIds,ChrBandTree-method childrenOf childrenOf,ChrBandTree,character-method ChrBandTree-class geneIds,ChrBandTree-method level2nodes level2nodes,ChrBandTree,character-method level2nodes,ChrBandTree,numeric-method lgeneIds lgeneIds,ChrBandTree-method parentOf parentOf,ChrBandTree,character-method show,ChrBandTree-method treeLevels treeLevels,ChrBandTree-method |
| Class "ChrMapHyperGParams" | ChrMapHyperGParams-class conditional,ChrMapHyperGParams-method conditional<-,ChrMapHyperGParams,logical-method |
| Class "ChrMapHyperGResult" | ChrMapHyperGResult-class conditional,ChrMapHyperGResult-method |
| Class "ChrMapLinearMParams" | ChrMapLinearMParams-class |
| Class "ChrMapLinearMResult" | chrGraph,ChrMapLinearMResult-method ChrMapLinearMResult-class |
| Class "DatPkg" | AffyDatPkg-class ArabidopsisDatPkg-class DatPkg-class DatPkgFactory DatPkgFactory,character-method DatPkgFactory,ChipDb-method DatPkgFactory,OBOCollection,GeneSetCollection-method DatPkgFactory,OrgDb-method GeneSetCollectionDatPkg GO2AllProbes GO2AllProbes,DatPkg-method GO2AllProbes,GeneSetCollectionDatPkg-method GO2AllProbes,Org.XX.egDatPkg-method GO2AllProbes,YeastDatPkg-method ID2EntrezID ID2EntrezID,AffyDatPkg-method ID2EntrezID,ArabidopsisDatPkg-method ID2EntrezID,GeneSetCollectionDatPkg-method ID2EntrezID,Org.XX.egDatPkg-method ID2EntrezID,YeastDatPkg-method ID2GO ID2GO,DatPkg-method ID2GO,GeneSetCollectionDatPkg-method ID2KEGG ID2KEGG,DatPkg-method ID2KEGG,GeneSetCollectionDatPkg-method isDBDatPkg,DatPkg-method isDBDatPkg,GeneSetCollectionDatPkg-method KEGG2AllProbes KEGG2AllProbes,DatPkg-method KEGG2AllProbes,GeneSetCollectionDatPkg-method OBOCollectionDatPkg OBOCollectionDatPkg-class Org.XX.egDatPkg-class organism,DatPkg-method organism,GeneSetCollectionDatPkg-method YeastDatPkg-class |
| Extract estimated effect sizes | effectSize |
| Display a sample node from each level of a ChrBandTree object | exampleLevels |
| Compute per category summary statistics | findAMstats |
| A function to print pathway names given their numeric ID. | getPathNames |
| Class "GOHyperGParams" | annotation,GOHyperGParams-method categoryName,GOHyperGParams-method conditional,GOHyperGParams-method conditional<-,GOHyperGParams,logical-method GOHyperGParams-class ontology,GOHyperGParams-method ontology<-,GOHyperGParams,character-method show,GOHyperGParams-method |
| Helper function for constructing a GOHyperGParams objects or KEGGHyperGParams objects from a GeneSetCollection | GSEAGOHyperGParams GSEAKEGGHyperGParams |
| Permutation p-values for GSEA | gseattperm |
| Hypergeometric (gene set enrichment) tests on character vectors. | hyperg hyperg,character-method hyperg,list-method |
| Class "HyperGParams" | annotation,HyperGParams-method annotation<-,HyperGParams,character-method categoryName categoryName,HyperGParams-method conditional conditional,HyperGParams-method conditional<- geneIds,HyperGParams-method geneIds<- geneIds<-,HyperGParams,ANY-method geneIds<-,HyperGParams,logical-method HyperGParams-class initialize,HyperGParams-method makeValidParams,HyperGParams-method ontology ontology,HyperGParams-method ontology<- organism,HyperGParams-method pvalueCutoff,HyperGParams-method pvalueCutoff<- pvalueCutoff<-,HyperGParams-method show,HyperGParams-method testDirection,HyperGParams-method testDirection<- testDirection<-,HyperGParams-method universeGeneIds universeGeneIds,HyperGParams-method |
| Accessors for HyperGResult Objects | annotation annotation,HyperGResultBase-method chrGraph chrGraph,ChrMapHyperGResult-method description description,HyperGResultBase-method expectedCounts expectedCounts,ChrMapHyperGResult-method expectedCounts,HyperGResult-method geneCounts geneCounts,HyperGResultBase-method geneIds geneIds,HyperGResultBase-method geneIdsByCategory geneIdsByCategory,HyperGResultBase-method geneIdUniverse geneIdUniverse,ChrMapHyperGResult-method geneIdUniverse,HyperGResult-method geneMappedCount geneMappedCount,HyperGResultBase-method htmlReport htmlReport,HyperGResultBase-method htmlReport,KEGGHyperGResult-method htmlReport,PFAMHyperGResult-method HyperGResult-accessors oddsRatios oddsRatios,ChrMapHyperGResult-method oddsRatios,HyperGResult-method organism,HyperGResult-method pvalueCutoff pvalueCutoff,HyperGResultBase-method pvalues pvalues,ChrMapHyperGResult-method pvalues,HyperGResult-method sigCategories sigCategories,HyperGResultBase-method summary,HyperGResultBase-method summary,KEGGHyperGResult-method summary,PFAMHyperGResult-method testDirection testDirection,HyperGResultBase-method testName testName,HyperGResultBase-method universeCounts universeCounts,HyperGResultBase-method universeMappedCount universeMappedCount,HyperGResultBase-method |
| Class "HyperGResult" | HyperGResult-class KEGGHyperGResult-class PFAMHyperGResult-class |
| Class "HyperGResultBase" | conditional,HyperGResultBase-method HyperGResultBase-class show,HyperGResultBase-method |
| Hypergeometric Test for association of categories and genes | hyperGTest hyperGTest,ChrMapHyperGParams-method hyperGTest,HyperGParams-method hyperGTest,KEGGHyperGParams-method hyperGTest,PFAMHyperGParams-method |
| Class "KEGGHyperGParams" and "PFAMHyperGParams" | KEGGHyperGParams-class PFAMHyperGParams-class |
| Class "LinearMParams" | annotation,LinearMParams-method annotation<-,LinearMParams,character-method categoryName,LinearMParams-method conditional,LinearMParams-method conditional<-,LinearMParams,logical-method geneIds,LinearMParams-method geneIds<-,LinearMParams,ANY-method LinearMParams-class pvalueCutoff,LinearMParams-method pvalueCutoff<-,LinearMParams-method show,LinearMParams-method testDirection,LinearMParams-method testDirection<-,LinearMParams-method universeGeneIds,LinearMParams-method |
| Class "LinearMResult" | effectSize,LinearMResult-method LinearMResult-class pvalues,LinearMResult-method summary,LinearMResult-method |
| Class "LinearMResultBase" | annotation,LinearMResultBase-method conditional,LinearMResultBase-method description,LinearMResultBase-method geneIds,LinearMResultBase-method geneIdsByCategory,LinearMResultBase-method geneIdUniverse,LinearMResultBase-method geneMappedCount,LinearMResultBase-method LinearMResultBase-class pvalueCutoff,LinearMResultBase-method show,LinearMResultBase-method sigCategories,LinearMResultBase-method summary,LinearMResultBase-method testDirection,LinearMResultBase-method testName,LinearMResultBase-method universeCounts,LinearMResultBase-method universeMappedCount,LinearMResultBase-method |
| A linear model-based test to detect enrichment of unusual genes in categories | linearMTest linearMTest,LinearMParams-method |
| Create a graph representing chromosome band annotation data | makeChrBandGraph |
| A function to make the contrast vectors needed for EBarrays | makeEBcontr |
| Non-standard Generic for Checking Validity of Parameter Objects | makeValidParams |
| Mapping chromosome bands to genes | makeChrBandGSC makeChrBandInciMat MAPAmat |
| Create a new ChrBandTree object | ChrBandTreeFromGraph NewChrBandTree |
| Class "OBOHyperGParams" | annotation,OBOHyperGParams-method categoryName,OBOHyperGParams-method conditional,OBOHyperGParams-method conditional<-,OBOHyperGParams,logical-method OBOHyperGParams OBOHyperGParams-class show,OBOHyperGParams-method |
| Map probe IDs to MAP regions. | probes2MAP |
| A function to map probe identifiers to pathways. | probes2Path |
| A simple function to compute a permutation t-test. | ttperm |
| Return a vector of gene identifiers with category annotations | universeBuilder universeBuilder,GOHyperGParams-method universeBuilder,KEGGHyperGParams-method universeBuilder,OBOHyperGParams-method universeBuilder,PFAMHyperGParams-method |
