# Disease Ontology Semantic and Enrichment analysis

## Documentation for package ‘DOSE’ version 3.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.
barplot.enrichResult | barplot
clusterSim | clusterSim
cnetplot | cnetplot method
cnetplot-method | cnetplot method
cnetplot_internal | cnetplot_internal
computeIC | compute information content
DataSet | Datasets
DGN_EXTID2PATHID | Datasets
DGN_PATHID2EXTID | Datasets
DGN_PATHID2NAME | Datasets
DO2ALLEG | Datasets
DO2EG | Datasets
DOIC | 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.
doSim | doSim
dotbl | Datasets
dotplot | dotplot method
dotplot-method | dotplot method
EG2ALLDO | Datasets
EG2DO | Datasets
EG2DOLite | Datasets
enrichDGN | Enrichment analysis based on the DisGeNET (<URL: http://www.disgenet.org/>)
enrichDGNv | enrichDGN
enrichDO | DO Enrichment Analysis
enricher_internal | enrich.internal
enrichMap | enrichMap
enrichNCG | enrichNCG
enrichResult-class | Class "enrichResult" This class represents the result of enrichment analysis.
EXTID2NAME | EXTID2NAME
fortify.enrichResult | fortify
gene2DO | convert Gene ID to DO Terms
geneID | geneID generic
geneInCategory | geneInCategory generic
geneList | Datasets
geneSim | geneSim
gseahResult-class | Class "gseaResult" This class represents the result of GSEA analysis
gseaplot | visualize analyzing result of GSEA
gseaResult-class | Class "gseaResult" This class represents the result of GSEA analysis
GSEA_internal | GSEA_internal
gseDGN | DisGeNET Gene Set Enrichment Analysis
gseDO | DO Gene Set Enrichment Analysis
gseNCG | NCG Gene Set Enrichment Analysis
gsfilter | gsfilter
gsInfo | gsInfo
list2graph | convert gene IDs to igraph object
mclusterSim | mclusterSim
NCG_EXTID2PATHID | Datasets
NCG_PATHID2EXTID | Datasets
NCG_PATHID2NAME | 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
ridgeplot | ridgeplot
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
theme_dose | theme_dose
upsetplot | upsetplot method
upsetplot-method | upsetplot method
VDGN_EXTID2PATHID | Datasets
VDGN_PATHID2EXTID | Datasets
VDGN_PATHID2NAME | Datasets