Documentations

Functions for analysis and visualisations

These analysis and visualisation functions are used to process ontologies (and annotations), to do enrichment analysis, to calculate semantic similarity between annotated domains based on ontology term semantic similarity, and to perform random walk with restart upon domain-domain (semantic) networks. Most of analyses are supported by high-performance parallel computing.

• dcDAGannotate
  Function to generate a subgraph of a direct acyclic graph (DAG) induced by the input annotation data
• dcRDataLoader
  Function to load dcGOR built-in RData
• dcConverter
  Function to convert an object between graph classes
• dcEnrichment
  Function to conduct ontology enrichment analysis given a group of domains
• visEnrichment
  Function to visualise enrichment analysis outputs in the context of the ontology hierarchy
• dcDAGdomainSim
  Function to calculate pair-wise semantic similarity between domains based on a direct acyclic graph (DAG) with annotated data
• 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

Functions for built-in (customised) data building

These functions are used to build objects of S4 classes 'InfoDataFrame', 'Anno' and 'Onto' from user-customised input data (domains, ontologies and annotations).

• dcBuildInfoDataFrame
  Function to build an object of the S4 class InfoDataframe from an input file
• dcBuildAnno
  Function to build an object of the S4 class Anno from input files
• dcBuildOnto
  Function to build an object of the S4 class Onto from input files

Definitions for S4 classes and methods

These documentations are to help understand S4 classes and methods defined in the package.

• InfoDataFrame-class(InfoDataFrame)
  Definition for S4 class InfoDataFrame
• InfoDataFrame-method(Data, Data,InfoDataFrame-method, [,InfoDataFrame,ANY,ANY,ANY-method, [,InfoDataFrame-method, colNames, colNames,InfoDataFrame-method, data.frame2InfoDataFrame, dim,InfoDataFrame-method, dimLabels, dimLabels,InfoDataFrame-method, ncol, ncol,InfoDataFrame-method, nrow, nrow,InfoDataFrame-method, rowNames, rowNames,InfoDataFrame-method, show,InfoDataFrame-method)
  Methods defined for S4 class InfoDataFrame
• AnnoData-class(AnnoData)
  Definition for VIRTUAL S4 class AnnoData
• Anno-class(Anno)
  Definition for S4 class Anno
• Anno-method([,Anno,ANY,ANY,ANY-method, [,Anno-method, annoData, annoData,Anno-method, dData, dData,Anno-method, dgCMatrix2Anno, dim,Anno-method, domainData, domainData,Anno-method, domainNames, domainNames,Anno-method, matrix2Anno, show,Anno-method, tData, tData,Anno-method, termData, termData,Anno-method, termNames, termNames,Anno-method)
  Methods defined for S4 class Anno
• AdjData-class(AdjData)
  Definition for VIRTUAL S4 class AdjData
• Onto-class(Onto)
  Definition for S4 class Onto
• Onto-method([,Onto,ANY,ANY,ANY-method, [,Onto-method, adjMatrix, adjMatrix,Onto-method, dgCMatrix2Onto, dim,Onto-method, matrix2Onto, nInfo, nInfo,Onto-method, nodeInfo, nodeInfo,Onto-method, nodeNames, nodeNames,Onto-method, show,Onto-method, term_distance, term_distance,Onto-method, term_id, term_id,Onto-method, term_name, term_name,Onto-method, term_namespace, term_namespace,Onto-method)
  Methods defined for S4 class Onto
• Eoutput-class(Eoutput)
  Definition for S4 class Eoutput
• Eoutput-method(adjp, adjp,Eoutput-method, pvalue, pvalue,Eoutput-method, show,Eoutput-method, view, view,Eoutput-method, write, write,Eoutput-method, zscore, zscore,Eoutput-method)
  Methods defined for S4 class Eoutput
• Dnetwork-class(Dnetwork)
  Definition for S4 class Dnetwork
• Dnetwork-method([,Dnetwork,ANY,ANY,ANY-method, [,Dnetwork-method, adjMatrix,Dnetwork-method, description, description,Dnetwork-method, dgCMatrix2Dnetwork, dim,Dnetwork-method, id, id,Dnetwork-method, level, level,Dnetwork-method, matrix2Dnetwork, nInfo,Dnetwork-method, nodeInfo,Dnetwork-method, nodeNames,Dnetwork-method, show,Dnetwork-method)
  Methods defined for S4 class Dnetwork
• Cnetwork-class(Cnetwork)
  Definition for S4 class Cnetwork
• Cnetwork-method([,Cnetwork,ANY,ANY,ANY-method, [,Cnetwork-method, adjMatrix,Cnetwork-method, dgCMatrix2Cnetwork, dim,Cnetwork-method, matrix2Cnetwork, nInfo,Cnetwork-method, nodeInfo,Cnetwork-method, nodeNames,Cnetwork-method, show,Cnetwork-method)
  Methods defined for S4 class Cnetwork
• Coutput-class(Coutput)
  Definition for S4 class Coutput
• Coutput-method(adjp,Coutput-method, cnetwork, cnetwork,Coutput-method, pvalue,Coutput-method, ratio, ratio,Coutput-method, show,Coutput-method, write,Coutput-method, zscore,Coutput-method)
  Methods defined for S4 class Coutput

Ontologies mainly including open biomedical ontology (obo)

These ontologies each are represented as a direct acyclic graph (DAG). DAG is stored as an object of class 'Onto'.

• onto.GOBP
  Gene Ontology Biological Process (GOBP).
• onto.GOMF
  Gene Ontology Molecular Function (GOMF).
• onto.GOCC
  Gene Ontology Cellular Component (GOCC).
• onto.DO
  Disease Ontology (DO).
• onto.HPPA
  Human Phenotype Phenotypic Abnormality (HPPA).
• onto.HPMI
  Human Phenotype Mode of Inheritance (HPMI).
• onto.HPON
  Human Phenotype ONset and clinical course (HPON).
• onto.MP
  Mammalian Phenotype (MP).
• onto.EC
  Enzyme Commission (EC).
• onto.KW
  UniProtKB KeyWords (KW).
• onto.UP
  UniProtKB UniPathway (UP).

SCOP domain superfamilies and their annotations by ontologies

These R objects are about SCOP domain superfamilies (sf) and their annotations by various ontologies, derived from the dcGO database.

• SCOP.sf
  SCOP domain superfamilies (sf).
• SCOP.sf2GOBP
  Annotations of SCOP domain superfamilies (sf) by Gene Ontology Biological Process (GOBP).
• SCOP.sf2GOMF
  Annotations of SCOP domain superfamilies (sf) by Gene Ontology Molecular Function (GOMF).
• SCOP.sf2GOCC
  Annotations of SCOP domain superfamilies (sf) by Gene Ontology Cellular Component (GOCC).
• SCOP.sf2DO
  Annotations of SCOP domain superfamilies (sf) by Disease Ontology (DO).
• SCOP.sf2HPPA
  Annotations of SCOP domain superfamilies (sf) by Human Phenotype Phenotypic Abnormality (HPPA).
• 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.sf2MP
  Annotations of SCOP domain superfamilies (sf) by Mammalian Phenotype (MP).
• SCOP.sf2EC
  Annotations of SCOP domain superfamilies (sf) by Enzyme Commission (EC).
• SCOP.sf2KW
  Annotations of SCOP domain superfamilies (sf) by UniProtKB KeyWords (KW).
• SCOP.sf2UP
  Annotations of SCOP domain superfamilies (sf) by UniProtKB UniPathway (UP).

SCOP domain families and their annotations by ontologies

These R objects are about SCOP domain families (fa) and their annotations by various ontologies, derived from the dcGO database.

• SCOP.fa
  SCOP domain families (fa).
• SCOP.fa2GOBP
  Annotations of SCOP domain families (fa) by Gene Ontology Biological Process (GOBP).
• SCOP.fa2GOMF
  Annotations of SCOP domain families (fa) by Gene Ontology Molecular Function (GOMF).
• SCOP.fa2GOCC
  Annotations of SCOP domain families (fa) by Gene Ontology Cellular Component (GOCC).
• SCOP.fa2DO
  Annotations of SCOP domain families (fa) by Disease Ontology (DO).
• SCOP.fa2HPPA
  Annotations of SCOP domain families (fa) by Human Phenotype Phenotypic Abnormality (HPPA).
• 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.fa2MP
  Annotations of SCOP domain families (fa) by Mammalian Phenotype (MP).
• SCOP.fa2EC
  Annotations of SCOP domain families (fa) by Enzyme Commission (EC).
• SCOP.fa2KW
  Annotations of SCOP domain families (fa) by UniProtKB KeyWords (KW).
• SCOP.fa2UP
  Annotations of SCOP domain families (fa) by UniProtKB UniPathway (UP).

Pfam domains and their annotations by ontologies

These R objects are about Pfam domains (Pfam) and their annotations by Gene Ontology (GO).

• Pfam
  Pfam domains (Pfam).
• Pfam2GOBP
  Annotations of Pfam domains by Gene Ontology Biological Process (GOBP).
• Pfam2GOMF
  Annotations of Pfam domains by Gene Ontology Molecular Function (GOMF).
• Pfam2GOCC
  Annotations of Pfam domains by Gene Ontology Cellular Component (GOCC).

InterPro domains and their annotations by ontologies

These R objects are about InterPro domains (InterPro) and their annotations by Gene Ontology (GO).

• InterPro
  InterPro domains (InterPro).
• InterPro2GOBP
  Annotations of InterPro domains by Gene Ontology Biological Process (GOBP).
• InterPro2GOMF
  Annotations of InterPro domains by Gene Ontology Molecular Function (GOMF).
• InterPro2GOCC
  Annotations of InterPro domains by Gene Ontology Cellular Component (GOCC).

Rfam RNA families and their annotations by ontologies

These R objects are about Rfam RNA families (Rfam) and their annotations by Gene Ontology (GO).

• Rfam
  RNA families (Rfam).
• Rfam2GOBP
  Annotations of Rfam RNA families by Gene Ontology Biological Process (GOBP).
• Rfam2GOMF
  Annotations of Rfam RNA families by Gene Ontology Molecular Function (GOMF).
• Rfam2GOCC
  Annotations of Rfam RNA families by Gene Ontology Cellular Component (GOCC).

Complete domains (domain-ome) in Eukaryotic tree of life (eTOL)

These databases and functions are used for domain-centric genome analysis in Eukaryotes. Note: these domains are defined as SCOP domain superfamilies.

• Ancestral_domainome
  Ancestral superfamily domain repertoires in Eukaryotes
• eTOL
  eukaryotic Tree Of Life (eTOL)
• dcAncestralML
  Function to reconstruct ancestral discrete states using fast maximum likelihood algorithm
• dcAncestralMP
  Function to reconstruct ancestral discrete states using maximum parsimony algorithm
• 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
• dcDuplicated
  Function to determine the duplicated patterns from input data matrix

Functions for domain-centric ontology creation and ontology term predictions

These functions are used for creating domain-centric ontology, which in turn is used for predicting domain-centric ontology terms from input protein domain architectures.

• dcSplitArch
  Function to obtain a list of features via splitting an input architecture
• dcFunArgs
  Function to assign (and evaluate) arguments with default values for an input function
• dcSparseMatrix
  Function to create a sparse matrix for an input file with three columns
• dcList2Matrix
  Function to convert a list into a matrix containing three columns
• dcSupraBetter
  Function to find supra-domains with better scores than their individual domains
• dcAlgo
  Function to apply dcGO algorithm to infer domain-centric ontology
• dcAlgoPropagate
  Function to propagate ontology annotations according to an input file
• dcAlgoPredict
  Function to predict ontology terms given domain architectures (including individual domains)
• dcAlgoPredictMain
  Function to predict ontology terms given an input file containing domain architectures (including individual domains)
• dcAlgoPredictGenome
  Function to predict ontology terms for genomes with domain architectures (including individual domains)
• dcAlgoPredictPR
  Function to assess the prediction performance via Precision-Recall (PR) analysis
• dcRWRpredict
  Function to perform RWR-based ontology term predictions from input known annotations and an input graph
• dcNaivePredict
  Function to perform naive prediction from input known annotations

Databases used for ontology term predictions

These databases contain ontology annotations (along with hypergeometric scores) for domains and domain combinations, which are then used for domain-centric ontology term predictions.

• Feature2GOBP.sf
  Annotations and scores between SCOP domains/combinations (at the superfamily level; sf) and Gene Ontology Biological Process (GOBP).
• Feature2GOMF.sf
  Annotations and scores between SCOP domains/combinations (at the superfamily level; sf) and Gene Ontology Molecular Function (GOMF).
• Feature2GOCC.sf
  Annotations and scores between SCOP domains/combinations (at the superfamily level; sf) and Gene Ontology Cellular Component (GOCC).
• Feature2HPPA.sf
  Annotations and scores between SCOP domains/combinations (at the superfamily level; sf) and Human Phenotype Phenotypic Abnormality (HPPA).
• Feature2GOBP.pfam
  Annotations and scores between Pfam domains/combinations and Gene Ontology Biological Process (GOBP).
• Feature2GOMF.pfam
  Annotations and scores between Pfam domains/combinations and Gene Ontology Molecular Function (GOMF).
• Feature2GOCC.pfam
  Annotations and scores between Pfam domains/combinations and Gene Ontology Cellular Component (GOCC).
• Feature2HPPA.pfam
  Annotations and scores between Pfam domains/combinations and Human Phenotype Phenotypic Abnormality (HPPA).
• Feature2GOBP.interpro
  Annotations and scores between InterPro domains and Gene Ontology Biological Process (GOBP).
• Feature2GOMF.interpro
  Annotations and scores between InterPro domains and Gene Ontology Molecular Function (GOMF).
• Feature2GOCC.interpro
  Annotations and scores between InterPro domains and Gene Ontology Cellular Component (GOCC).
• Feature2HPPA.interpro
  Annotations and scores between InterPro domains and Human Phenotype Phenotypic Abnormality (HPPA).