Disease Ontology Semantic and Enrichment analysis

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Documentation for package ‘DOSE’ version 3.24.2

• 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.
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
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
gseNCG	NCG Gene Set Enrichment Analysis
gsfilter	gsfilter
mclusterSim	mclusterSim
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