Disease Ontology Semantic and Enrichment analysis


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Documentation for package ‘DOSE’ version 1.2.1

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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 Get all background External ID.
cnetplot plot gene net by categories
combineScores combining similarity matrix to similarity score
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
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.
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
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
infoContentMethod information content based methods
Info_Contents_human_DO Datasets Information content and DO term to entrez gene IDs mapping
list2graph convert gene IDs to igraph object
loadICdata Load IC data
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.
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
wangMethod wangMethod