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 |