simAnn/NAMESPACE at main · guokai8/simAnn · GitHub

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# Generated by roxygen2: do not edit by hand
useDynLib(simAnn, .registration=TRUE)
importFrom(Rcpp, evalCpp)
exportPattern("^[[:alpha:]]+")
S3method(print,OntologyTree)
S3method(print,TermClusters)
S3method(print,summary.TermClusters)
export(AllICMethod)
export(AllSimMethod)
export(OntologyTree)
export(addOntologyTerms)
export(addTermStats)
export(buildGOTree)
export(buildKEGGTree)
export(buildOntologyTree)
export(calculateAncestorSim)
export(calculateAnnotationIC)
export(calculateFaithSim)
export(calculateGOGOSim)
export(calculateIC)
export(calculateLinSim)
export(calculateRelevanceSim)
export(calculateResnikSim)
export(calculateSimICSim)
export(calculateTermSimilarity)
export(calculateUniversalSim)
export(calculateWangIC)
export(calculateWangSim)
export(ch_index)
export(clusterComplex)
export(clusterST)
export(clusterSTW)
export(convertToIgraph)
export(db_index)
export(df2annolist)
export(findMICA)
export(findMICAterm)
export(findMaxAncestor)
export(fromGraphToOntology)
export(getChildCount)
export(getChildren)
export(getGenePathwayMapping)
export(getOffspringCount)
export(getParentCount)
export(getParents)
export(getTermStats)
export(hasTerms)
export(isLeaf)
export(leaves)
export(listTermStats)
export(nEdges)
export(nLeaves)
export(nTerms)
export(pickThreshold)
export(plotClusterHeatmap)
export(plotClusterNetwork)
export(plotOntologyTree)
export(removeTermStats)
export(root)
export(simterm)
export(simtermW)
export(summary.OntologyTree)
export(summary.TermClusters)
export(term2id)
export(terms)
export(threshold_cluster)
export(updateAnnotationsR)
exportClasses(OntologyTree)
exportMethods(show)
exportMethods(summary)
import(AnnotationDbi)
import(GO.db)
import(ggplot2)
importFrom(GO.db,GOBPCHILDREN)
importFrom(GO.db,GOCCCHILDREN)
importFrom(GO.db,GOMFCHILDREN)
importFrom(KEGGREST,keggLink)
importFrom(cluster,silhouette)
importFrom(ggplot2,theme_void)
importFrom(ggraph,create_layout)
importFrom(ggraph,geom_edge_link)
importFrom(ggraph,geom_node_point)
importFrom(ggraph,geom_node_text)
importFrom(ggraph,ggraph)
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,cluster_louvain)
importFrom(igraph,cluster_walktrap)
importFrom(igraph,components)
importFrom(igraph,degree)
importFrom(igraph,distances)
importFrom(igraph,get.edgelist)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,graph_from_edgelist)
importFrom(igraph,is.dag)
importFrom(igraph,is.directed)
importFrom(igraph,membership)
importFrom(igraph,modularity)
importFrom(igraph,plot.igraph)
importFrom(igraph,set_edge_attr)
importFrom(methods,as)
importFrom(methods,is)
importFrom(pheatmap,pheatmap)
importFrom(stats,cor)
importFrom(stats,fisher.test)
importFrom(stats,hclust)
importFrom(stats,p.adjust)