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 |
barplot.enrichResult | barplot |
clusterSim | clusterSim |
cnetplot | cnetplot method |
cnetplot-method | cnetplot method |
cnetplot_internal | cnetplot_internal |
computeIC | compute information content |
DataSet | Datasets |
DO2ALLEG | Datasets |
DO2EG | Datasets |
DOLite2EG | Datasets |
DOLiteTerm | Datasets |
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 |
doSim | doSim |
dotplot | dotplot method |
dotplot-method | dotplot method |
EG2ALLDO | Datasets |
EG2DO | Datasets |
EG2DOLite | Datasets |
enrich.internal | enrich.internal |
enrichDO | DO Enrichment Analysis |
enrichMap | enrichMap |
enrichNCG | enrichNCG |
enrichResult-class | Class "enrichResult" This class represents the result of enrichment analysis. |
EXTID2NAME | EXTID2NAME |
EXTID2TERMID | EXTID2TERMID |
fortify.enrichResult | fortify |
fortify.gseaResult | fortify.gseaResult |
gene2DO | convert Gene ID to DO Terms |
geneList | Datasets |
geneSim | geneSim |
getALLEG | getALLEG |
getGeneSet | getGeneSet |
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 |
Info_Contents_human_DO | Datasets |
list2graph | convert gene IDs to igraph object |
mclusterSim | mclusterSim |
NCG_DOSE_Env | Datasets |
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 |
TERMID2EXTID | TERMID2EXTID |
theme_dose | theme_dose |