Disease Analysis toolkit for gene set; Computation of similarities between DO terms and disease similarity between gene products; Module detection among the gene set and multilayer annotation for each module.


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Documentation for package ‘DOSim’ version 2.2

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DOSim-package DOSim package
annoModule Multilayer annotation for each module
calcTermSim internal functions
cutreeConstant internal functions
detectModule Detect modules from gene set
DOEnrichment DO enrichment analysis
DOGenes Get a vector of genes annotated by current DO
DOGraph internal functions
DOSim DOSim package
DOSimEnv Disease Ontology enviroment object
filterDO Filter DO
getAncestors Get a list of all ancestors associated to each DO term
getChildren Get a list of all direct children of each DO term
getDefaultBackground Get a vector of genes annotated by current DO
getDisjAnc internal functions
getDisjCommAnc Get disjoint common ancestors.
getDisjCommAncSim internal functions
getDoAnno Get gene list associated to each DO term
getDOGraph Get DO graph with specified DO terms at its leave.
getDoTerm Get DO term's name
getGeneSim Compute disease similarity for genes base on DO
getGIC internal functions
getGSim internal functions
getMinimumSubsumer Compute minimum subsumer (the most information common ancestor:MICA) of two DO terms
getOffsprings Get all offspring associated with each DO term
getParents Get direct parents for each DO term
getShortestPath Get the shortest path between two terms
getSimLch internal functions
getSimPath internal functions
getSimWang internal functions
getTermSim Get pairwise DO term similarities.
initialize_DOSimEnv internal functions
internal internal functions
normalize.kernel internal functions
obesity 361 obesity related genes' similarity matrix
precomputeTermSims internal functions
saveAnnoModule Detect modules from gene set
saveModule Save the module result
viewModule Display modules