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A C D E I L M N O P R S T V W Z misc
| AdjData | Definition for VIRTUAL S4 class AdjData |
| AdjData-class | Definition for VIRTUAL S4 class AdjData |
| adjMatrix | Methods defined for S4 class Onto |
| adjMatrix-method | Methods defined for S4 class Cnetwork |
| adjMatrix-method | Methods defined for S4 class Dnetwork |
| adjMatrix-method | Methods defined for S4 class Onto |
| adjp | Methods defined for S4 class Eoutput |
| adjp-method | Methods defined for S4 class Coutput |
| adjp-method | Methods defined for S4 class Eoutput |
| Ancestral_domainome | Ancestral superfamily domain repertoires in Eukaryotes |
| Anno | Definition for S4 class Anno |
| Anno-class | Definition for S4 class Anno |
| Anno-method | Methods defined for S4 class Anno |
| AnnoData | Definition for VIRTUAL S4 class AnnoData |
| annoData | Methods defined for S4 class Anno |
| AnnoData-class | Definition for VIRTUAL S4 class AnnoData |
| annoData-method | Methods defined for S4 class Anno |
| Cnetwork | Definition for S4 class Cnetwork |
| cnetwork | Methods defined for S4 class Coutput |
| Cnetwork-class | Definition for S4 class Cnetwork |
| Cnetwork-method | Methods defined for S4 class Cnetwork |
| cnetwork-method | Methods defined for S4 class Coutput |
| colNames | Methods defined for S4 class InfoDataFrame |
| colNames-method | Methods defined for S4 class InfoDataFrame |
| Coutput | Definition for S4 class Coutput |
| Coutput-class | Definition for S4 class Coutput |
| Coutput-method | Methods defined for S4 class Coutput |
| Data | Methods defined for S4 class InfoDataFrame |
| Data-method | Methods defined for S4 class InfoDataFrame |
| data.frame2InfoDataFrame | Methods defined for S4 class InfoDataFrame |
| 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) |
| dcAlgoPropagate | Function to propogate 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 |
| 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 |
| 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 |
| dcTreeConnectivity | Function to calculate the sparse connectivity matrix between parents and children from a phylo-formatted phylogenetic tree |
| dData | Methods defined for S4 class Anno |
| dData-method | Methods defined for S4 class Anno |
| description | Methods defined for S4 class Dnetwork |
| description-method | Methods defined for S4 class Dnetwork |
| dgCMatrix2Anno | Methods defined for S4 class Anno |
| dgCMatrix2Cnetwork | Methods defined for S4 class Cnetwork |
| dgCMatrix2Dnetwork | Methods defined for S4 class Dnetwork |
| dgCMatrix2Onto | Methods defined for S4 class Onto |
| dim-method | Methods defined for S4 class Anno |
| dim-method | Methods defined for S4 class Cnetwork |
| dim-method | Methods defined for S4 class Dnetwork |
| dim-method | Methods defined for S4 class InfoDataFrame |
| dim-method | Methods defined for S4 class Onto |
| dimLabels | Methods defined for S4 class InfoDataFrame |
| dimLabels-method | Methods defined for S4 class InfoDataFrame |
| Dnetwork | Definition for S4 class Dnetwork |
| Dnetwork-class | Definition for S4 class Dnetwork |
| Dnetwork-method | Methods defined for S4 class Dnetwork |
| domainData | Methods defined for S4 class Anno |
| domainData-method | Methods defined for S4 class Anno |
| domainNames | Methods defined for S4 class Anno |
| domainNames-method | Methods defined for S4 class Anno |
| Eoutput | Definition for S4 class Eoutput |
| Eoutput-class | Definition for S4 class Eoutput |
| Eoutput-method | Methods defined for S4 class Eoutput |
| eTOL | eukaryotic Tree Of Life (eTOL) |
| id | Methods defined for S4 class Dnetwork |
| id-method | Methods defined for S4 class Dnetwork |
| InfoDataFrame | Definition for S4 class InfoDataFrame |
| 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). |
| level | Methods defined for S4 class Dnetwork |
| level-method | Methods defined for S4 class Dnetwork |
| matrix2Anno | Methods defined for S4 class Anno |
| matrix2Cnetwork | Methods defined for S4 class Cnetwork |
| matrix2Dnetwork | Methods defined for S4 class Dnetwork |
| matrix2Onto | Methods defined for S4 class Onto |
| ncol | Methods defined for S4 class InfoDataFrame |
| ncol-method | Methods defined for S4 class InfoDataFrame |
| nInfo | Methods defined for S4 class Onto |
| nInfo-method | Methods defined for S4 class Cnetwork |
| nInfo-method | Methods defined for S4 class Dnetwork |
| nInfo-method | Methods defined for S4 class Onto |
| nodeInfo | Methods defined for S4 class Onto |
| nodeInfo-method | Methods defined for S4 class Cnetwork |
| nodeInfo-method | Methods defined for S4 class Dnetwork |
| nodeInfo-method | Methods defined for S4 class Onto |
| nodeNames | Methods defined for S4 class Onto |
| nodeNames-method | Methods defined for S4 class Cnetwork |
| nodeNames-method | Methods defined for S4 class Dnetwork |
| nodeNames-method | Methods defined for S4 class Onto |
| nrow | Methods defined for S4 class InfoDataFrame |
| nrow-method | Methods defined for S4 class InfoDataFrame |
| Onto | Definition for S4 class Onto |
| Onto-class | Definition for S4 class Onto |
| Onto-method | Methods defined for S4 class Onto |
| 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). |
| 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). |
| pvalue | Methods defined for S4 class Eoutput |
| pvalue-method | Methods defined for S4 class Coutput |
| pvalue-method | Methods defined for S4 class Eoutput |
| ratio | Methods defined for S4 class Coutput |
| ratio-method | Methods defined for S4 class Coutput |
| 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). |
| rowNames | Methods defined for S4 class InfoDataFrame |
| rowNames-method | Methods defined for S4 class InfoDataFrame |
| 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). |
| show-method | Methods defined for S4 class Anno |
| show-method | Methods defined for S4 class Cnetwork |
| show-method | Methods defined for S4 class Coutput |
| show-method | Methods defined for S4 class Dnetwork |
| show-method | Methods defined for S4 class Eoutput |
| show-method | Methods defined for S4 class InfoDataFrame |
| show-method | Methods defined for S4 class Onto |
| tData | Methods defined for S4 class Anno |
| tData-method | Methods defined for S4 class Anno |
| termData | Methods defined for S4 class Anno |
| termData-method | Methods defined for S4 class Anno |
| termNames | Methods defined for S4 class Anno |
| termNames-method | Methods defined for S4 class Anno |
| term_distance | Methods defined for S4 class Onto |
| term_distance-method | Methods defined for S4 class Onto |
| term_id | Methods defined for S4 class Onto |
| term_id-method | Methods defined for S4 class Onto |
| term_name | Methods defined for S4 class Onto |
| term_name-method | Methods defined for S4 class Onto |
| term_namespace | Methods defined for S4 class Onto |
| term_namespace-method | Methods defined for S4 class Onto |
| view | Methods defined for S4 class Eoutput |
| view-method | Methods defined for S4 class Eoutput |
| visEnrichment | Function to visualise enrichment analysis outputs in the context of the ontology hierarchy |
| write | Methods defined for S4 class Eoutput |
| write-method | Methods defined for S4 class Coutput |
| write-method | Methods defined for S4 class Eoutput |
| zscore | Methods defined for S4 class Eoutput |
| zscore-method | Methods defined for S4 class Coutput |
| zscore-method | Methods defined for S4 class Eoutput |
| [-method | Methods defined for S4 class Anno |
| [-method | Methods defined for S4 class Cnetwork |
| [-method | Methods defined for S4 class Dnetwork |
| [-method | Methods defined for S4 class InfoDataFrame |
| [-method | Methods defined for S4 class Onto |