Package: annaffy 1.79.0
Colin A. Smith
annaffy: Annotation tools for Affymetrix biological metadata
Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.
Authors:
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annaffy.pdf |annaffy.html✨
annaffy/json (API)
| # Install 'annaffy' in R: |
| install.packages('annaffy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- aafExpr - Sample ExpressionSet used for demonstration purposes
On BioConductor:annaffy-1.79.0(bioc 3.21)annaffy-1.78.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
onechannelmicroarrayannotationgopathwaysreportwriting
Last updated 2 months agofrom:5617a63610. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win | WARNING | Dec 18 2024 |
| R-4.5-linux | WARNING | Dec 18 2024 |
| R-4.4-win | WARNING | Dec 18 2024 |
| R-4.4-mac | WARNING | Dec 18 2024 |
| R-4.3-win | WARNING | Dec 18 2024 |
| R-4.3-mac | WARNING | Dec 18 2024 |
Exports:aaf.handleraafChromLocaafChromosomeaafCytobandaafDescriptionaafGenBankaafGOaafLocusLinkaafPathwayaafProbeaafPubMedaafSearchGOaafSearchTextaafSymbolaafTableaafTableAnnaafTableFrameaafTableIntcolnamesgetCSSgetHTMLgetTDgetTextgetURLis.annpkgprobeidsprobeids<-saveHTMLsaveTextselectorWidgetshow
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapgenericsGenomeInfoDbGenomeInfoDbDataglueGO.dbhttrIRangesjsonliteKEGGRESTlifecyclememoisemimeopensslpkgconfigplogrpngR6rlangRSQLiteS4VectorssysUCSC.utilsvctrsXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Handle feching annotation data columns | aaf.handler |
| Constructor for aafChromLoc objects | aafChromLoc |
| Class aafChromLoc, a class for gene chromosome locations | aafChromLoc-class |
| Constructor for aafChromosome objects | aafChromosome |
| Class aafChromosome, a class for gene chromosome assignments | aafChromosome-class |
| Constructor for aafCytoband objects | aafCytoband |
| Class aafCytoband, a class for cytoband data | aafCytoband-class getText,aafCytoband-method getURL,aafCytoband-method show,aafCytoband-method |
| Constructor for aafDescription objects | aafDescription |
| Class aafDescription, a class for gene descriptions | aafDescription-class |
| Sample ExpressionSet used for demonstration purposes | aafExpr |
| Constructor for aafGenBank objects | aafGenBank |
| Class aafGenBank, a class for GenBank accession numbers | aafGenBank-class getURL,aafGenBank-method |
| Constructor for aafGO objects | aafGO |
| Class aafGO, a class for gene ontology ids | aafGO-class getCSS,aafGO-method getHTML,aafGO-method getTD,aafGO-method getText,aafGO-method getURL,aafGO-method |
| Class aafGOItem, a class for gene ontology id elements | aafGOItem aafGOItem-class getHTML,aafGOItem-method getText,aafGOItem-method getURL,aafGOItem-method show,aafGOItem-method |
| Class aafIntensity, a class for gene expression values | aafIntensity aafIntensity-class getTD,aafIntensity-method |
| Class aafList, a specialized subclass of list | aafList aafList-class getCSS,aafList-method getHTML,aafList-method getTD,aafList-method getText,aafList-method getURL,aafList-method show,aafList-method [,aafList-method |
| Constructor for aafLocusLink objects | aafLocusLink |
| Class aafLocusLink, a class for LocusLink ids | aafLocusLink-class getURL,aafLocusLink-method |
| Constructor for aafPathway objects | aafPathway |
| Class aafPathway, a class for KEGG pathway ids | aafPathway-class getCSS,aafPathway-method getHTML,aafPathway-method getTD,aafPathway-method getText,aafPathway-method getURL,aafPathway-method |
| Class aafPathwayItem, a class for KEGG pathway id elements | aafPathwayItem aafPathwayItem-class getHTML,aafPathwayItem-method getText,aafPathwayItem-method getURL,aafPathwayItem-method show,aafPathwayItem-method |
| Constructor for aafProbe objects | aafProbe |
| Class aafProbe, a class for Probe ids | aafProbe-class getURL,aafProbe-method |
| Constructor for aafPubMed objects | aafPubMed |
| Class aafPubMed, a class for PubMed ids | aafPubMed-class getCSS,aafPubMed-method getHTML,aafPubMed-method getTD,aafPubMed-method getURL,aafPubMed-method |
| Find probe ids corresponding to GO ids | aafSearchGO |
| Search metadata annotation text | aafSearchText |
| Class aafSigned, a class for signed numerical data | aafSigned aafSigned-class getCSS,aafSigned-method getTD,aafSigned-method |
| Constructor for aafSymbol objects | aafSymbol |
| Class aafSymbol, a class for gene symbols | aafSymbol-class |
| Constructor for aafTable objects | aafTable |
| Class aafTable, a tabular microarray data class | $.aafTable aafTable-class colnames colnames,aafTable-method colnames<- colnames<-,aafTable-method dim.aafTable merge.aafTable probeids probeids,aafTable-method probeids<- probeids<-,aafTable-method rbind.aafTable saveHTML saveHTML,aafTable-method saveText saveText,aafTable-method [,aafTable-method [[,aafTable-method |
| Constructor for aafTable objects from annotation data | aafTableAnn |
| Constructor for aafTable objects from data frames | aafTableFrame |
| Constructor for aafTable objects from ExpressionSets | aafTableInt |
| Methods for function getCSS | getCSS getCSS,ANY-method getCSS-methods |
| Methods for function getHTML | getHTML getHTML,ANY-method getHTML-methods |
| Methods for function getTD | getTD getTD,ANY-method getTD-methods |
| Methods for function getText | getText getText,ANY-method getText-methods |
| Methods for function getURL | getURL getURL,ANY-method getURL-methods |
| Determine if packages contain annotation | is.annpkg |
| Dialog to select items from a list | selectorWidget |
