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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. |
| AL1 | Datasets Information content and DO term to entrez gene IDs mapping |
| AL1expr | Datasets Information content and DO term to entrez gene IDs mapping |
| ALLEXTID | Get all background External ID. |
| cnetplot | 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 |
| DOParams-class | Class "DOParams" This class contains parameters for calculating DO semantic similarity among DO term or Gene list. |
| 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. |
| enrichResult-class | Class "enrichResult" This class represents the result of DO enrichment analysis. |
| EXTID2NAME | EXTID2NAME |
| EXTID2TERMID | Mapping External ID to Ontology Term ID |
| gene2DO | convert Gene ID to DO Terms |
| geneSim | geneSim |
| 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 |
| plot | plot method |
| plot-method | Class "enrichResult" This class represents the result of DO enrichment analysis. |
| plot-method | plot method |
| rebuildAnnoData | rebuiding annotation data |
| setReadable | Methods mapping gene ID to gene symbol for 'enrichResult' instance |
| setReadable-methods | Methods mapping gene ID to gene symbol for 'enrichResult' instance |
| setReadable<- | Methods mapping gene ID to gene symbol for 'enrichResult' instance |
| setReadable<--method | Class "enrichResult" This class represents the result of DO enrichment analysis. |
| setReadable<--method | Methods mapping gene ID to gene symbol for 'enrichResult' instance |
| show | show method |
| show-method | Class "enrichResult" This class represents the result of DO enrichment analysis. |
| sim | Methods for calculating semantic similarity |
| sim-method | Class "DOParams" This class contains parameters for calculating DO semantic similarity among DO term or Gene list. |
| simplot | simplot |
| summary | summary method |
| summary-method | Class "enrichResult" This class represents the result of DO enrichment analysis. |
| TERM2NAME | Mapping Ontology Term ID to Name Symbol or Description |
| TERMID2EXTID | Mapping Ontology Term ID to External ID |