AdjData-class           Definition for VIRTUAL S4 class AdjData
Ancestral_domainome     Ancestral superfamily domain repertoires in
                        Eukaryotes
Anno-class              Definition for S4 class Anno
Anno-method             Methods defined for S4 class Anno
AnnoData-class          Definition for VIRTUAL S4 class AnnoData
Cnetwork-class          Definition for S4 class Cnetwork
Cnetwork-method         Methods defined for S4 class Cnetwork
Coutput-class           Definition for S4 class Coutput
Coutput-method          Methods defined for S4 class Coutput
Dnetwork-class          Definition for S4 class Dnetwork
Dnetwork-method         Methods defined for S4 class Dnetwork
Eoutput-class           Definition for S4 class Eoutput
Eoutput-method          Methods defined for S4 class Eoutput
InfoDataFrame-class     Definition for S4 class InfoDataFrame
InfoDataFrame-method    Methods defined for S4 class InfoDataFrame
InterPro                InterPro domains (InterPro).
InterPro2GOBP           Annotations of InterPro domains by Gene
                        Ontology Biological Process (GOBP).
InterPro2GOCC           Annotations of InterPro domains by Gene
                        Ontology Cellular Component (GOCC).
InterPro2GOMF           Annotations of InterPro domains by Gene
                        Ontology Molecular Function (GOMF).
Onto-class              Definition for S4 class Onto
Onto-method             Methods defined for S4 class Onto
Pfam                    Pfam domains (Pfam).
Pfam2GOBP               Annotations of Pfam domains by Gene Ontology
                        Biological Process (GOBP).
Pfam2GOCC               Annotations of Pfam domains by Gene Ontology
                        Cellular Component (GOCC).
Pfam2GOMF               Annotations of Pfam domains by Gene Ontology
                        Molecular Function (GOMF).
Rfam                    RNA families (Rfam).
Rfam2GOBP               Annotations of Rfam RNA families by Gene
                        Ontology Biological Process (GOBP).
Rfam2GOCC               Annotations of Rfam RNA families by Gene
                        Ontology Cellular Component (GOCC).
Rfam2GOMF               Annotations of Rfam RNA families by Gene
                        Ontology Molecular Function (GOMF).
SCOP.fa                 SCOP domain families (fa).
SCOP.fa2DO              Annotations of SCOP domain families (fa) by
                        Disease Ontology (DO).
SCOP.fa2GOBP            Annotations of SCOP domain families (fa) by
                        Gene Ontology Biological Process (GOBP).
SCOP.fa2GOCC            Annotations of SCOP domain families (fa) by
                        Gene Ontology Cellular Component (GOCC).
SCOP.fa2GOMF            Annotations of SCOP domain families (fa) by
                        Gene Ontology Molecular Function (GOMF).
SCOP.fa2HPMI            Annotations of SCOP domain families (fa) by
                        Human Phenotype Mode of Inheritance (HPMI).
SCOP.fa2HPON            Annotations of SCOP domain families (fa) by
                        Human Phenotype ONset and clinical course
                        (HPON).
SCOP.fa2HPPA            Annotations of SCOP domain families (fa) by
                        Human Phenotype Phenotypic Abnormality (HPPA).
SCOP.fa2MP              Annotations of SCOP domain families (fa) by
                        Mammalian Phenotype (MP).
SCOP.sf                 SCOP domain superfamilies (sf).
SCOP.sf2DO              Annotations of SCOP domain superfamilies (sf)
                        by Disease Ontology (DO).
SCOP.sf2GOBP            Annotations of SCOP domain superfamilies (sf)
                        by Gene Ontology Biological Process (GOBP).
SCOP.sf2GOCC            Annotations of SCOP domain superfamilies (sf)
                        by Gene Ontology Cellular Component (GOCC).
SCOP.sf2GOMF            Annotations of SCOP domain superfamilies (sf)
                        by Gene Ontology Molecular Function (GOMF).
SCOP.sf2HPMI            Annotations of SCOP domain superfamilies (sf)
                        by Human Phenotype Mode of Inheritance (HPMI).
SCOP.sf2HPON            Annotations of SCOP domain superfamilies (sf)
                        by Human Phenotype ONset and clinical course
                        (HPON).
SCOP.sf2HPPA            Annotations of SCOP domain superfamilies (sf)
                        by Human Phenotype Phenotypic Abnormality
                        (HPPA).
SCOP.sf2MP              Annotations of SCOP domain superfamilies (sf)
                        by Mammalian Phenotype (MP).
dcAlgo                  Function to apply dcGO algorithm to infer
                        domain-centric ontology
dcAlgoPredict           Function to predict ontology terms given domain
                        architectures (including individual domains)
dcAlgoPredictGenome     Function to predict ontology terms for genomes
                        with domain architectures (including individual
                        domains)
dcAlgoPredictMain       Function to predict ontology terms given an
                        input file containing domain architectures
                        (including individual domains)
dcAlgoPredictPR         Function to assess the prediction performance
                        via Precision-Recall (PR) analysis
dcAlgoPropagate         Function to propagate ontology annotations
                        according to an input file
dcAncestralML           Function to reconstruct ancestral discrete
                        states using fast maximum likelihood algorithm
dcAncestralMP           Function to reconstruct ancestral discrete
                        states using maximum parsimony algorithm
dcBuildAnno             Function to build an object of the S4 class
                        Anno from input files
dcBuildInfoDataFrame    Function to build an object of the S4 class
                        InfoDataframe from an input file
dcBuildOnto             Function to build an object of the S4 class
                        Onto from input files
dcConverter             Function to convert an object between graph
                        classes
dcDAGannotate           Function to generate a subgraph of a direct
                        acyclic graph (DAG) induced by the input
                        annotation data
dcDAGdomainSim          Function to calculate pair-wise semantic
                        similarity between domains based on a direct
                        acyclic graph (DAG) with annotated data
dcDuplicated            Function to determine the duplicated patterns
                        from input data matrix
dcEnrichment            Function to conduct ontology enrichment
                        analysis given a group of domains
dcFunArgs               Function to assign (and evaluate) arguments
                        with default values for an input function
dcList2Matrix           Function to convert a list into a matrix
                        containing three columns
dcNaivePredict          Function to perform naive prediction from input
                        known annotations
dcRDataLoader           Function to load dcGOR built-in RData
dcRWRpipeline           Function to setup a pipeine to estimate
                        RWR-based contact strength between samples from
                        an input domain-sample data matrix and an input
                        graph
dcRWRpredict            Function to perform RWR-based ontology term
                        predictions from input known annotations and an
                        input graph
dcSparseMatrix          Function to create a sparse matrix for an input
                        file with three columns
dcSplitArch             Function to obtain a list of features via
                        splitting an input architecture
dcSubtreeClade          Function to extract a subtree under a given
                        clade from a phylo-formatted phylogenetic tree
dcSubtreeTips           Function to extract a tip-induced subtree from
                        a phylo-formatted phylogenetic tree
dcSupraBetter           Function to find supra-domains with better
                        scores than their individual domains
dcTreeConnectivity      Function to calculate the sparse connectivity
                        matrix between parents and children from a
                        phylo-formatted phylogenetic tree
eTOL                    eukaryotic Tree Of Life (eTOL)
onto.DO                 Disease Ontology (DO).
onto.GOBP               Gene Ontology Biological Process (GOBP).
onto.GOCC               Gene Ontology Cellular Component (GOCC).
onto.GOMF               Gene Ontology Molecular Function (GOMF).
onto.HPMI               Human Phenotype Mode of Inheritance (HPMI).
onto.HPON               Human Phenotype ONset and clinical course
                        (HPON).
onto.HPPA               Human Phenotype Phenotypic Abnormality (HPPA).
onto.MP                 Mammalian Phenotype (MP).
visEnrichment           Function to visualise enrichment analysis
                        outputs in the context of the ontology
                        hierarchy
