dcGOR: Analysis of Ontologies and Protein Domain Annotations

There lacks a package for analysing domain-centric ontologies and annotations, particularly those in the dcGO database. The dcGO (http://supfam.org/SUPERFAMILY/dcGO) is a comprehensive domain-centric database for annotating protein domains using a panel of ontologies including Gene Ontology. With the package, users are expected to analyse and visualise domain-centric ontologies and annotations. Supported analyses include but are not limited to: easy access to a wide range of ontologies and their domain-centric annotations; able to build customised ontologies and annotations; domain-based enrichment analysis and visualisation; construction of a domain (semantic similarity) network according to ontology annotations; significance analysis for estimating a contact (statistical significance) network via Random Walk with Restart; and high-performance parallel computing. The new functionalities are: 1) to create domain-centric ontologies; 2) to predict ontology terms for input protein sequences (precisely domain content in the form of architectures) plus to assess the predictions; 3) to reconstruct ancestral discrete characters using maximum likelihood/parsimony.

AuthorHai Fang and Julian Gough
Bioconductor views Bioinformatics
Date of publication2016-04-25 11:13:02
MaintainerHai Fang <hfang@well.ox.ac.uk>
http://cran.r-project.org/package=dcGOR, http://dcgor.r-forge.r-project.org, https://github.com/hfang-bristol/dcGOR

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Man pages

AdjData-class: Definition for VIRTUAL S4 class AdjData

Ancestral_domainome: Ancestral superfamily domain repertoires in Eukaryotes

Anno-class: Definition for S4 class Anno

AnnoData-class: Definition for VIRTUAL S4 class AnnoData

Anno-method: Methods defined for S4 class Anno

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

dcAlgo: Function to apply dcGO algorithm to infer domain-centric...

dcAlgoPredict: Function to predict ontology terms given domain architectures...

dcAlgoPredictGenome: Function to predict ontology terms for genomes with domain...

dcAlgoPredictMain: Function to predict ontology terms given an input file...

dcAlgoPredictPR: Function to assess the prediction performance via...

dcAlgoPropagate: Function to propagate ontology annotations according to an...

dcAncestralML: Function to reconstruct ancestral discrete states using fast...

dcAncestralMP: Function to reconstruct ancestral discrete states using...

dcBuildAnno: Function to build an object of the S4 class Anno from input...

dcBuildInfoDataFrame: Function to build an object of the S4 class InfoDataframe...

dcBuildOnto: Function to build an object of the S4 class Onto from input...

dcConverter: Function to convert an object between graph classes

dcDAGannotate: Function to generate a subgraph of a direct acyclic graph...

dcDAGdomainSim: Function to calculate pair-wise semantic similarity between...

dcDuplicated: Function to determine the duplicated patterns from input data...

dcEnrichment: Function to conduct ontology enrichment analysis given a...

dcFunArgs: Function to assign (and evaluate) arguments with default...

dcList2Matrix: Function to convert a list into a matrix containing three...

dcNaivePredict: Function to perform naive prediction from input known...

dcRDataLoader: Function to load dcGOR built-in RData

dcRWRpipeline: Function to setup a pipeine to estimate RWR-based contact...

dcRWRpredict: Function to perform RWR-based ontology term predictions from...

dcSparseMatrix: Function to create a sparse matrix for an input file with...

dcSplitArch: Function to obtain a list of features via splitting an input...

dcSubtreeClade: Function to extract a subtree under a given clade from a...

dcSubtreeTips: Function to extract a tip-induced subtree from a...

dcSupraBetter: Function to find supra-domains with better scores than their...

dcTreeConnectivity: Function to calculate the sparse connectivity matrix between...

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

eTOL: eukaryotic Tree Of Life (eTOL)

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...

InterPro2GOCC: Annotations of InterPro domains by Gene Ontology Cellular...

InterPro2GOMF: Annotations of InterPro domains by Gene Ontology Molecular...

Onto-class: Definition 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-method: Methods defined for S4 class Onto

onto.MP: Mammalian Phenotype (MP).

Pfam: Pfam domains (Pfam).

Pfam2GOBP: Annotations of Pfam domains by Gene Ontology Biological...

Pfam2GOCC: Annotations of Pfam domains by Gene Ontology Cellular...

Pfam2GOMF: Annotations of Pfam domains by Gene Ontology Molecular...

Rfam: RNA families (Rfam).

Rfam2GOBP: Annotations of Rfam RNA families by Gene Ontology Biological...

Rfam2GOCC: Annotations of Rfam RNA families by Gene Ontology Cellular...

Rfam2GOMF: Annotations of Rfam RNA families by Gene Ontology Molecular...

SCOP.fa: SCOP domain families (fa).

SCOP.fa2DO: Annotations of SCOP domain families (fa) by Disease Ontology...

SCOP.fa2GOBP: Annotations of SCOP domain families (fa) by Gene Ontology...

SCOP.fa2GOCC: Annotations of SCOP domain families (fa) by Gene Ontology...

SCOP.fa2GOMF: Annotations of SCOP domain families (fa) by Gene Ontology...

SCOP.fa2HPMI: Annotations of SCOP domain families (fa) by Human Phenotype...

SCOP.fa2HPON: Annotations of SCOP domain families (fa) by Human Phenotype...

SCOP.fa2HPPA: Annotations of SCOP domain families (fa) by Human Phenotype...

SCOP.fa2MP: Annotations of SCOP domain families (fa) by Mammalian...

SCOP.sf: SCOP domain superfamilies (sf).

SCOP.sf2DO: Annotations of SCOP domain superfamilies (sf) by Disease...

SCOP.sf2GOBP: Annotations of SCOP domain superfamilies (sf) by Gene...

SCOP.sf2GOCC: Annotations of SCOP domain superfamilies (sf) by Gene...

SCOP.sf2GOMF: Annotations of SCOP domain superfamilies (sf) by Gene...

SCOP.sf2HPMI: Annotations of SCOP domain superfamilies (sf) by Human...

SCOP.sf2HPON: Annotations of SCOP domain superfamilies (sf) by Human...

SCOP.sf2HPPA: Annotations of SCOP domain superfamilies (sf) by Human...

SCOP.sf2MP: Annotations of SCOP domain superfamilies (sf) by Mammalian...

visEnrichment: Function to visualise enrichment analysis outputs in the...


AdjData Man page
AdjData-class Man page
adjMatrix Man page
adjMatrix,Cnetwork-method Man page
adjMatrix,Dnetwork-method Man page
adjMatrix,Onto-method Man page
adjp Man page
adjp,Coutput-method Man page
adjp,Eoutput-method Man page
Ancestral_domainome Man page
Anno Man page
[,Anno,ANY,ANY,ANY-method Man page
Anno-class Man page
annoData Man page
AnnoData Man page
annoData,Anno-method Man page
AnnoData-class Man page
[,Anno-method Man page
Anno-method Man page
cnetwork Man page
Cnetwork Man page
[,Cnetwork,ANY,ANY,ANY-method Man page
Cnetwork-class Man page
cnetwork,Coutput-method Man page
[,Cnetwork-method Man page
Cnetwork-method Man page
colNames Man page
colNames,InfoDataFrame-method Man page
Coutput Man page
Coutput-class Man page
Coutput-method Man page
Data Man page
data.frame2InfoDataFrame Man page
Data,InfoDataFrame-method Man page
dcAlgo Man page
dcAlgoPredict Man page
dcAlgoPredictGenome Man page
dcAlgoPredictMain Man page
dcAlgoPredictPR Man page
dcAlgoPropagate Man page
dcAncestralML Man page
dcAncestralMP Man page
dcBuildAnno Man page
dcBuildInfoDataFrame Man page
dcBuildOnto Man page
dcConverter Man page
dcDAGannotate Man page
dcDAGdomainSim Man page
dcDuplicated Man page
dcEnrichment Man page
dcFunArgs Man page
dcList2Matrix Man page
dcNaivePredict Man page
dcRDataLoader Man page
dcRWRpipeline Man page
dcRWRpredict Man page
dcSparseMatrix Man page
dcSplitArch Man page
dcSubtreeClade Man page
dcSubtreeTips Man page
dcSupraBetter Man page
dcTreeConnectivity Man page
dData Man page
dData,Anno-method Man page
description Man page
description,Dnetwork-method Man page
dgCMatrix2Anno Man page
dgCMatrix2Cnetwork Man page
dgCMatrix2Dnetwork Man page
dgCMatrix2Onto Man page
dim,Anno-method Man page
dim,Cnetwork-method Man page
dim,Dnetwork-method Man page
dim,InfoDataFrame-method Man page
dimLabels Man page
dimLabels,InfoDataFrame-method Man page
dim,Onto-method Man page
Dnetwork Man page
[,Dnetwork,ANY,ANY,ANY-method Man page
Dnetwork-class Man page
[,Dnetwork-method Man page
Dnetwork-method Man page
domainData Man page
domainData,Anno-method Man page
domainNames Man page
domainNames,Anno-method Man page
Eoutput Man page
Eoutput-class Man page
Eoutput-method Man page
eTOL Man page
id Man page
id,Dnetwork-method Man page
InfoDataFrame Man page
[,InfoDataFrame,ANY,ANY,ANY-method Man page
InfoDataFrame-class Man page
[,InfoDataFrame-method Man page
InfoDataFrame-method Man page
InterPro Man page
InterPro2GOBP Man page
InterPro2GOCC Man page
InterPro2GOMF Man page
level Man page
level,Dnetwork-method Man page
matrix2Anno Man page
matrix2Cnetwork Man page
matrix2Dnetwork Man page
matrix2Onto Man page
ncol Man page
ncol,InfoDataFrame-method Man page
nInfo Man page
nInfo,Cnetwork-method Man page
nInfo,Dnetwork-method Man page
nInfo,Onto-method Man page
nodeInfo Man page
nodeInfo,Cnetwork-method Man page
nodeInfo,Dnetwork-method Man page
nodeInfo,Onto-method Man page
nodeNames Man page
nodeNames,Cnetwork-method Man page
nodeNames,Dnetwork-method Man page
nodeNames,Onto-method Man page
nrow Man page
nrow,InfoDataFrame-method Man page
Onto Man page
[,Onto,ANY,ANY,ANY-method Man page
Onto-class Man page
onto.DO Man page
onto.GOBP Man page
onto.GOCC Man page
onto.GOMF Man page
onto.HPMI Man page
onto.HPON Man page
onto.HPPA Man page
[,Onto-method Man page
Onto-method Man page
onto.MP Man page
Pfam Man page
Pfam2GOBP Man page
Pfam2GOCC Man page
Pfam2GOMF Man page
pvalue Man page
pvalue,Coutput-method Man page
pvalue,Eoutput-method Man page
ratio Man page
ratio,Coutput-method Man page
Rfam Man page
Rfam2GOBP Man page
Rfam2GOCC Man page
Rfam2GOMF Man page
rowNames Man page
rowNames,InfoDataFrame-method Man page
SCOP.fa Man page
SCOP.fa2DO Man page
SCOP.fa2GOBP Man page
SCOP.fa2GOCC Man page
SCOP.fa2GOMF Man page
SCOP.fa2HPMI Man page
SCOP.fa2HPON Man page
SCOP.fa2HPPA Man page
SCOP.fa2MP Man page
SCOP.sf Man page
SCOP.sf2DO Man page
SCOP.sf2GOBP Man page
SCOP.sf2GOCC Man page
SCOP.sf2GOMF Man page
SCOP.sf2HPMI Man page
SCOP.sf2HPON Man page
SCOP.sf2HPPA Man page
SCOP.sf2MP Man page
show,Anno-method Man page
show,Cnetwork-method Man page
show,Coutput-method Man page
show,Dnetwork-method Man page
show,Eoutput-method Man page
show,InfoDataFrame-method Man page
show,Onto-method Man page
tData Man page
tData,Anno-method Man page
termData Man page
termData,Anno-method Man page
term_distance Man page
term_distance,Onto-method Man page
term_id Man page
term_id,Onto-method Man page
term_name Man page
term_name,Onto-method Man page
termNames Man page
termNames,Anno-method Man page
term_namespace Man page
term_namespace,Onto-method Man page
view Man page
view,Eoutput-method Man page
visEnrichment Man page
write Man page
write,Coutput-method Man page
write,Eoutput-method Man page
zscore Man page
zscore,Coutput-method Man page
zscore,Eoutput-method Man page


R/ClassMethod-dcGOR.r R/dcAlgo.r R/dcAlgoPredict.r R/dcAlgoPredictGenome.r R/dcAlgoPredictMain.r R/dcAlgoPredictPR.r R/dcAlgoPropagate.r R/dcAncestralML.r R/dcAncestralMP.r R/dcBuildAnno.r R/dcBuildInfoDataFrame.r R/dcBuildOnto.r R/dcConverter.r R/dcDAGannotate.r R/dcDAGdomainSim.r R/dcDuplicated.r R/dcEnrichment.r R/dcFunArgs.r R/dcList2Matrix.r R/dcNaivePredict.r R/dcRDataLoader.r R/dcRWRpipeline.r R/dcRWRpredict.r R/dcSparseMatrix.r R/dcSplitArch.r R/dcSubtreeClade.r R/dcSubtreeTips.r R/dcSupraBetter.r R/dcTreeConnectivity.r R/visEnrichment.r
inst/staticdocs/demo/AlgoPred.r inst/staticdocs/demo/Basu.r inst/staticdocs/demo/Customisation.r inst/staticdocs/demo/Fang.r inst/staticdocs/demo/Fang_paper.r
man/AdjData-class.Rd man/Ancestral_domainome.Rd man/Anno-class.Rd man/Anno-method.Rd man/AnnoData-class.Rd man/Cnetwork-class.Rd man/Cnetwork-method.Rd man/Coutput-class.Rd man/Coutput-method.Rd man/Dnetwork-class.Rd man/Dnetwork-method.Rd man/Eoutput-class.Rd man/Eoutput-method.Rd man/InfoDataFrame-class.Rd man/InfoDataFrame-method.Rd man/InterPro.Rd man/InterPro2GOBP.Rd man/InterPro2GOCC.Rd man/InterPro2GOMF.Rd man/Onto-class.Rd man/Onto-method.Rd man/Pfam.Rd man/Pfam2GOBP.Rd man/Pfam2GOCC.Rd man/Pfam2GOMF.Rd man/Rfam.Rd man/Rfam2GOBP.Rd man/Rfam2GOCC.Rd man/Rfam2GOMF.Rd man/SCOP.fa.Rd man/SCOP.fa2DO.Rd man/SCOP.fa2GOBP.Rd man/SCOP.fa2GOCC.Rd man/SCOP.fa2GOMF.Rd man/SCOP.fa2HPMI.Rd man/SCOP.fa2HPON.Rd man/SCOP.fa2HPPA.Rd man/SCOP.fa2MP.Rd man/SCOP.sf.Rd man/SCOP.sf2DO.Rd man/SCOP.sf2GOBP.Rd man/SCOP.sf2GOCC.Rd man/SCOP.sf2GOMF.Rd man/SCOP.sf2HPMI.Rd man/SCOP.sf2HPON.Rd man/SCOP.sf2HPPA.Rd man/SCOP.sf2MP.Rd man/dcAlgo.Rd man/dcAlgoPredict.Rd man/dcAlgoPredictGenome.Rd man/dcAlgoPredictMain.Rd man/dcAlgoPredictPR.Rd man/dcAlgoPropagate.Rd man/dcAncestralML.Rd man/dcAncestralMP.Rd man/dcBuildAnno.Rd man/dcBuildInfoDataFrame.Rd man/dcBuildOnto.Rd man/dcConverter.Rd man/dcDAGannotate.Rd man/dcDAGdomainSim.Rd man/dcDuplicated.Rd man/dcEnrichment.Rd man/dcFunArgs.Rd man/dcList2Matrix.Rd man/dcNaivePredict.Rd man/dcRDataLoader.Rd man/dcRWRpipeline.Rd man/dcRWRpredict.Rd man/dcSparseMatrix.Rd man/dcSplitArch.Rd man/dcSubtreeClade.Rd man/dcSubtreeTips.Rd man/dcSupraBetter.Rd man/dcTreeConnectivity.Rd man/eTOL.Rd man/onto.DO.Rd man/onto.GOBP.Rd man/onto.GOCC.Rd man/onto.GOMF.Rd man/onto.HPMI.Rd man/onto.HPON.Rd man/onto.HPPA.Rd man/onto.MP.Rd man/visEnrichment.Rd

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