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) |
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 |
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 |