# Disease Ontology Semantic and Enrichment analysis

## Documentation for package ‘DOSE’ version 3.28.1

- 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.
clusterSim | clusterSim
compareClusterResult-class | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
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.
doseSim | doSim
doSim | doSim
dotbl | Datasets
EG2ALLDO | Datasets
EG2DO | Datasets
EG2DOLite | Datasets
enrichDGN | Enrichment analysis based on the DisGeNET (<http://www.disgenet.org/>)
enrichDGNv | enrichDGN
enrichDO | DO Enrichment Analysis
enricher_internal | enrich.internal
enrichHPO | Enrichment analysis based on the DisGeNET (<http://www.disgenet.org/>)
enrichMPO | Enrichment analysis based on the DisGeNET (<http://www.disgenet.org/>)
enrichNCG | enrichNCG
enrichResult-class | Class "enrichResult" This class represents the result of enrichment analysis.
EXTID2NAME | EXTID2NAME
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
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
gseHPO | MPO Gene Set Enrichment Analysis
gseMPO | MPO Gene Set Enrichment Analysis
gseNCG | NCG Gene Set Enrichment Analysis
gsfilter | gsfilter
hpoSim | doSim
hpotbl | Datasets
mclusterSim | mclusterSim
mpoSim | doSim
mpotbl | Datasets
NCG_EXTID2PATHID | Datasets
NCG_PATHID2EXTID | Datasets
NCG_PATHID2NAME | Datasets
parse_ratio | parse_ratio
plot-method | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
rebuildAnnoData | rebuiding annotation data
setReadable | setReadable
show | show method
show-method | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
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 "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis.
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
VDGN_EXTID2PATHID | Datasets
VDGN_PATHID2EXTID | Datasets
VDGN_PATHID2NAME | Datasets