# Analysis of Ontologies and Protein Domain Annotations

## Documentation for package ‘dcGOR’ version 1.0.6

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A C D E I L M N O P R S T V W Z misc

## -- A --

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

## -- C --

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

## -- D --

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

## -- E --

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)

## -- I --

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).

## -- L --

level | Methods defined for S4 class Dnetwork
level-method | Methods defined for S4 class Dnetwork

## -- M --

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

## -- N --

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

## -- O --

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).

## -- P --

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

## -- R --

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

## -- S --

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

## -- T --

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

## -- V --

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

## -- W --

write | Methods defined for S4 class Eoutput
write-method | Methods defined for S4 class Coutput
write-method | Methods defined for S4 class Eoutput

## -- Z --

zscore | Methods defined for S4 class Eoutput
zscore-method | Methods defined for S4 class Coutput
zscore-method | Methods defined for S4 class Eoutput

## -- misc --

[-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