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 |
Get all background External ID. |
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. |
enrichResult-class |
Class "enrichResult" This class represents the result of enrichment analysis. |
EXTID2NAME |
EXTID2NAME |
EXTID2TERMID |
Mapping External ID to Ontology Term ID |
gene2DO |
convert Gene ID to DO Terms |
geneList |
Datasets Information content and DO term to entrez gene IDs mapping |
geneSim |
geneSim |
getALLEG |
getALLEG |
getGeneSet |
preparing geneSets for gene set enrichment analysis |
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 |
Mapping Ontology Term ID to Name Symbol or Description |
TERMID2EXTID |
Mapping Ontology Term ID to External ID |
theme_dose |
theme_dose |