Disease Ontology Semantic and Enrichment analysis


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Documentation for package ‘DOSE’ version 2.10.7

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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
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
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
fortify.gseaResult fortify.gseaResult
gene2DO convert Gene ID to DO Terms
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
gseDO DO Gene Set Enrichment Analysis
gseNCG NCG Gene Set Enrichment Analysis
gsfilter gsfilter
IC Datasets
Info_Contents_human_DO Datasets
list2graph convert gene IDs to igraph object
load_OrgDb load_OrgDb
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
theme_dose theme_dose
upsetplot upsetplot method
upsetplot-method upsetplot method