DOSim-package | DOSim package |
annoModule | Multilayer annotation for each module |
calcTermSim | 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 |
getTermSim | Get pairwise DO term similarities. |
initialize | internal functions |
internal | internal functions |
normalize.kernel | internal functions |
precomputeTermSims | internal functions |
saveAnnoModule | Detect modules from gene set |
saveModule | Save the module result |
viewModule | Display modules |