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. |
AL1 |
Datasets Information content and DO term to entrez gene IDs mapping |
AL1expr |
Datasets Information content and DO term to entrez gene IDs mapping |
ALLEXTID |
Get all background External ID. |
cnetplot |
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 |
DOParams-class |
Class "DOParams" This class contains parameters for calculating DO semantic similarity among DO term or Gene list. |
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 DO enrichment analysis. |
EXTID2NAME |
EXTID2NAME |
EXTID2TERMID |
Mapping External ID to Ontology Term ID |
gene2DO |
convert Gene ID to DO Terms |
geneSim |
geneSim |
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 |
plot |
plot method |
plot-method |
Class "enrichResult" This class represents the result of DO enrichment analysis. |
plot-method |
plot method |
rebuildAnnoData |
rebuiding annotation data |
setReadable |
Methods mapping gene ID to gene symbol for 'enrichResult' instance |
setReadable-methods |
Methods mapping gene ID to gene symbol for 'enrichResult' instance |
setReadable<- |
Methods mapping gene ID to gene symbol for 'enrichResult' instance |
setReadable<--method |
Class "enrichResult" This class represents the result of DO enrichment analysis. |
setReadable<--method |
Methods mapping gene ID to gene symbol for 'enrichResult' instance |
show |
show method |
show-method |
Class "enrichResult" This class represents the result of DO enrichment analysis. |
sim |
Methods for calculating semantic similarity |
sim-method |
Class "DOParams" This class contains parameters for calculating DO semantic similarity among DO term or Gene list. |
simplot |
simplot |
summary |
summary method |
summary-method |
Class "enrichResult" This class represents the result of DO enrichment analysis. |
TERM2NAME |
Mapping Ontology Term ID to Name Symbol or Description |
TERMID2EXTID |
Mapping Ontology Term ID to External ID |