Disease Ontology Semantic and Enrichment analysis


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Documentation for package ‘DOSE’ version 2.4.0

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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.
ALLEXTID ALLEXTID
ALLEXTID.DO ALLEXTID.DO
ALLEXTID.DOLite ALLEXTID.DOLite
barplot.enrichResult barplot
cnetplot cnetplot method
cnetplot-method cnetplot method
cnetplot-method Class "enrichResult" This class represents the result of enrichment analysis.
cnetplot.internal plot gene net by categories
computeIC compute information content
DataSet Datasets Information content and DO term to entrez gene IDs mapping
DO2ALLEG Datasets Information content and DO term to entrez gene IDs mapping
DO2EG Datasets Information content and DO term to entrez gene IDs mapping
DOLite2EG Datasets Information content and DO term to entrez gene IDs mapping
DOLiteTerm Datasets Information content and DO term to entrez gene IDs mapping
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 Information content and DO term to entrez gene IDs mapping
doSim doSim
EG2ALLDO Datasets Information content and DO term to entrez gene IDs mapping
EG2DO Datasets Information content and DO term to entrez gene IDs mapping
EG2DOLite Datasets Information content and DO term to entrez gene IDs mapping
enrich.internal enrich.internal
enrichDO DO Enrichment Analysis of a gene set.
enrichMap enrichMap
enrichResult-class Class "enrichResult" This class represents the result of enrichment analysis.
EXTID2NAME EXTID2NAME
EXTID2TERMID EXTID2TERMID
EXTID2TERMID.DO EXTID2TERMID.DO
EXTID2TERMID.DOLite EXTID2TERMID.DOLite
fortify.enrichResult fortify
fortify.gseaResult fortify.gseaResult
gene2DO convert Gene ID to DO Terms
geneList Datasets Information content and DO term to entrez gene IDs mapping
geneSim geneSim
getALLEG getALLEG
getGeneSet getGeneSet
getGeneSet.DO getGeneSet.DO
getGeneSet.DOLite getGeneSet.DOLite
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 Information content and DO term to entrez gene IDs mapping
Info_Contents_human_DO Datasets Information content and DO term to entrez gene IDs mapping
list2graph convert gene IDs to igraph object
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
TERM2NAME.DO TERM2NAME.DO
TERM2NAME.DOLite TERM2NAME.DOLite
TERMID2EXTID TERMID2EXTID
TERMID2EXTID.DO TERMID2EXTID.DO
TERMID2EXTID.DOLite TERMID2EXTID.DOLite
theme_dose theme_dose