# Disease Ontology Semantic and Enrichment analysis

## Documentation for package ‘DOSE’ version 2.8.3

- 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.
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