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| DOSE-package | Disease Ontology Semantic and Enrichment analysis Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring DO semantic similarities, and hypergeometric test for enrichment analysis. |
| ALLEXTID | ALLEXTID |
| ALLEXTID.DO | ALLEXTID.DO |
| ALLEXTID.DOLite | ALLEXTID.DOLite |
| barplot.enrichResult | barplot |
| cnetplot | cnetplot method |
| cnetplot-method | cnetplot method |
| cnetplot-method | Class "enrichResult" This class represents the result of enrichment analysis. |
| cnetplot.internal | plot gene net by categories |
| computeIC | compute information content |
| DataSet | Datasets Information content and DO term to entrez gene IDs mapping |
| DO2ALLEG | Datasets Information content and DO term to entrez gene IDs mapping |
| DO2EG | Datasets Information content and DO term to entrez gene IDs mapping |
| DOLite2EG | Datasets Information content and DO term to entrez gene IDs mapping |
| DOLiteTerm | Datasets Information content and DO term to entrez gene IDs mapping |
| DOSE | Disease Ontology Semantic and Enrichment analysis Implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring DO semantic similarities, and hypergeometric test for enrichment analysis. |
| DOSEEnv | Datasets Information content and DO term to entrez gene IDs mapping |
| doSim | doSim |
| EG2ALLDO | Datasets Information content and DO term to entrez gene IDs mapping |
| EG2DO | Datasets Information content and DO term to entrez gene IDs mapping |
| EG2DOLite | Datasets Information content and DO term to entrez gene IDs mapping |
| enrich.internal | enrich.internal |
| enrichDO | DO Enrichment Analysis of a gene set. |
| enrichMap | enrichMap |
| enrichResult-class | Class "enrichResult" This class represents the result of enrichment analysis. |
| EXTID2NAME | EXTID2NAME |
| EXTID2TERMID | EXTID2TERMID |
| EXTID2TERMID.DO | EXTID2TERMID.DO |
| EXTID2TERMID.DOLite | EXTID2TERMID.DOLite |
| fortify.enrichResult | fortify |
| fortify.gseaResult | fortify.gseaResult |
| gene2DO | convert Gene ID to DO Terms |
| geneList | Datasets Information content and DO term to entrez gene IDs mapping |
| geneSim | geneSim |
| getALLEG | getALLEG |
| getGeneSet | getGeneSet |
| getGeneSet.DO | getGeneSet.DO |
| getGeneSet.DOLite | getGeneSet.DOLite |
| gsea | gsea |
| gseahResult-class | Class "gseaResult" This class represents the result of GSEA analysis |
| gseAnalyzer | Gene Set Enrichment Analysis |
| gseaplot | visualize analyzing result of GSEA |
| gseaResult-class | Class "gseaResult" This class represents the result of GSEA analysis |
| IC | Datasets Information content and DO term to entrez gene IDs mapping |
| Info_Contents_human_DO | Datasets Information content and DO term to entrez gene IDs mapping |
| list2graph | convert gene IDs to igraph object |
| netplot | netplot |
| plot | plot method |
| plot-method | Class "enrichResult" This class represents the result of enrichment analysis. |
| plot-method | Class "gseaResult" This class represents the result of GSEA analysis |
| plot-method | plot method |
| rebuildAnnoData | rebuiding annotation data |
| scaleNodeColor | scaleNodeColor |
| setReadable | setReadable |
| setting.graph.attributes | setting.graph.attributes |
| show | show method |
| show-method | Class "enrichResult" This class represents the result of enrichment analysis. |
| show-method | Class "gseaResult" This class represents the result of GSEA analysis |
| simplot | simplot |
| summary | summary method |
| summary-method | Class "enrichResult" This class represents the result of enrichment analysis. |
| summary-method | Class "gseaResult" This class represents the result of GSEA analysis |
| TERM2NAME | TERM2NAME |
| TERM2NAME.DO | TERM2NAME.DO |
| TERM2NAME.DOLite | TERM2NAME.DOLite |
| TERMID2EXTID | TERMID2EXTID |
| TERMID2EXTID.DO | TERMID2EXTID.DO |
| TERMID2EXTID.DOLite | TERMID2EXTID.DOLite |
| theme_dose | theme_dose |