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.

Author
Hai Fang and Julian Gough
Date of publication
2015-07-27 10:52:03
Maintainer
Hai Fang <hfang@well.ox.ac.uk>
License
GPL-2
Version
1.0.6
URLs

View on CRAN

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...

Files in this package

dcGOR
dcGOR/inst
dcGOR/inst/staticdocs
dcGOR/inst/staticdocs/RData.md
dcGOR/inst/staticdocs/images
dcGOR/inst/staticdocs/images/dcGOR_logo.png
dcGOR/inst/staticdocs/images/dcGOR_workflow.png
dcGOR/inst/staticdocs/faq
dcGOR/inst/staticdocs/faq/List_faqs.txt
dcGOR/inst/staticdocs/demo
dcGOR/inst/staticdocs/demo/Customisation.r
dcGOR/inst/staticdocs/demo/List_demos.txt
dcGOR/inst/staticdocs/demo/Basu.r
dcGOR/inst/staticdocs/demo/Fang.r
dcGOR/inst/staticdocs/demo/AlgoPred.r
dcGOR/inst/staticdocs/demo/Fang_paper.r
dcGOR/inst/staticdocs/README.md
dcGOR/inst/staticdocs/INSTALLATIONs.md
dcGOR/inst/staticdocs/templates
dcGOR/inst/staticdocs/templates/navbar.html
dcGOR/inst/staticdocs/templates/footer.html
dcGOR/inst/staticdocs/docs.r
dcGOR/inst/staticdocs/CITATIONs.md
dcGOR/inst/CITATION
dcGOR/inst/NEWS
dcGOR/NAMESPACE
dcGOR/data
dcGOR/data/onto.GOBP.RData
dcGOR/data/Rfam.RData
dcGOR/data/InterPro2GOBP.RData
dcGOR/data/onto.HPMI.RData
dcGOR/data/onto.DO.RData
dcGOR/data/InterPro2GOMF.RData
dcGOR/data/SCOP.sf2MP.RData
dcGOR/data/SCOP.sf2HPPA.RData
dcGOR/data/SCOP.sf2GOCC.RData
dcGOR/data/SCOP.fa2HPPA.RData
dcGOR/data/Ancestral_domainome.RData
dcGOR/data/eTOL.RData
dcGOR/data/SCOP.fa2HPON.RData
dcGOR/data/onto.HPON.RData
dcGOR/data/SCOP.fa2DO.RData
dcGOR/data/onto.MP.RData
dcGOR/data/SCOP.sf2DO.RData
dcGOR/data/InterPro2GOCC.RData
dcGOR/data/InterPro.RData
dcGOR/data/SCOP.fa.RData
dcGOR/data/SCOP.sf2HPON.RData
dcGOR/data/Pfam2GOCC.RData
dcGOR/data/SCOP.sf2HPMI.RData
dcGOR/data/SCOP.fa2GOBP.RData
dcGOR/data/datalist
dcGOR/data/SCOP.fa2GOCC.RData
dcGOR/data/Rfam2GOBP.RData
dcGOR/data/onto.GOMF.RData
dcGOR/data/SCOP.sf2GOBP.RData
dcGOR/data/Rfam2GOCC.RData
dcGOR/data/SCOP.sf.RData
dcGOR/data/SCOP.fa2MP.RData
dcGOR/data/Rfam2GOMF.RData
dcGOR/data/SCOP.fa2HPMI.RData
dcGOR/data/SCOP.sf2GOMF.RData
dcGOR/data/Pfam2GOBP.RData
dcGOR/data/onto.HPPA.RData
dcGOR/data/Pfam2GOMF.RData
dcGOR/data/onto.GOCC.RData
dcGOR/data/SCOP.fa2GOMF.RData
dcGOR/data/Pfam.RData
dcGOR/R
dcGOR/R/dcAlgoPredictGenome.r
dcGOR/R/dcAncestralML.r
dcGOR/R/visEnrichment.r
dcGOR/R/dcFunArgs.r
dcGOR/R/dcList2Matrix.r
dcGOR/R/dcSplitArch.r
dcGOR/R/dcAlgoPredictPR.r
dcGOR/R/dcBuildInfoDataFrame.r
dcGOR/R/dcSparseMatrix.r
dcGOR/R/dcConverter.r
dcGOR/R/dcRDataLoader.r
dcGOR/R/dcNaivePredict.r
dcGOR/R/dcDAGannotate.r
dcGOR/R/dcDAGdomainSim.r
dcGOR/R/dcRWRpipeline.r
dcGOR/R/dcSubtreeClade.r
dcGOR/R/ClassMethod-dcGOR.r
dcGOR/R/dcRWRpredict.r
dcGOR/R/dcBuildAnno.r
dcGOR/R/dcAlgo.r
dcGOR/R/dcSupraBetter.r
dcGOR/R/dcAlgoPredict.r
dcGOR/R/dcEnrichment.r
dcGOR/R/dcAncestralMP.r
dcGOR/R/dcDuplicated.r
dcGOR/R/dcAlgoPredictMain.r
dcGOR/R/dcBuildOnto.r
dcGOR/R/dcTreeConnectivity.r
dcGOR/R/dcAlgoPropagate.r
dcGOR/R/dcSubtreeTips.r
dcGOR/MD5
dcGOR/DESCRIPTION
dcGOR/man
dcGOR/man/Anno-class.Rd
dcGOR/man/onto.DO.Rd
dcGOR/man/dcRWRpredict.Rd
dcGOR/man/Dnetwork-class.Rd
dcGOR/man/dcAlgoPredict.Rd
dcGOR/man/dcSplitArch.Rd
dcGOR/man/dcSubtreeTips.Rd
dcGOR/man/dcRDataLoader.Rd
dcGOR/man/InterPro2GOCC.Rd
dcGOR/man/dcBuildOnto.Rd
dcGOR/man/Rfam.Rd
dcGOR/man/SCOP.sf2HPMI.Rd
dcGOR/man/Rfam2GOCC.Rd
dcGOR/man/AdjData-class.Rd
dcGOR/man/SCOP.fa2GOBP.Rd
dcGOR/man/onto.GOCC.Rd
dcGOR/man/SCOP.sf2MP.Rd
dcGOR/man/SCOP.fa2HPPA.Rd
dcGOR/man/onto.HPPA.Rd
dcGOR/man/SCOP.fa2GOMF.Rd
dcGOR/man/AnnoData-class.Rd
dcGOR/man/dcAncestralMP.Rd
dcGOR/man/onto.MP.Rd
dcGOR/man/Coutput-method.Rd
dcGOR/man/Eoutput-class.Rd
dcGOR/man/dcDuplicated.Rd
dcGOR/man/Anno-method.Rd
dcGOR/man/visEnrichment.Rd
dcGOR/man/SCOP.fa.Rd
dcGOR/man/onto.GOBP.Rd
dcGOR/man/dcBuildAnno.Rd
dcGOR/man/InfoDataFrame-method.Rd
dcGOR/man/onto.HPMI.Rd
dcGOR/man/dcFunArgs.Rd
dcGOR/man/dcSparseMatrix.Rd
dcGOR/man/Ancestral_domainome.Rd
dcGOR/man/Pfam2GOMF.Rd
dcGOR/man/Eoutput-method.Rd
dcGOR/man/InterPro2GOMF.Rd
dcGOR/man/dcNaivePredict.Rd
dcGOR/man/InterPro2GOBP.Rd
dcGOR/man/onto.GOMF.Rd
dcGOR/man/InfoDataFrame-class.Rd
dcGOR/man/SCOP.fa2GOCC.Rd
dcGOR/man/dcSubtreeClade.Rd
dcGOR/man/dcEnrichment.Rd
dcGOR/man/dcSupraBetter.Rd
dcGOR/man/Cnetwork-method.Rd
dcGOR/man/SCOP.sf.Rd
dcGOR/man/onto.HPON.Rd
dcGOR/man/Pfam.Rd
dcGOR/man/SCOP.fa2HPON.Rd
dcGOR/man/dcConverter.Rd
dcGOR/man/Dnetwork-method.Rd
dcGOR/man/SCOP.sf2HPON.Rd
dcGOR/man/dcAlgoPredictGenome.Rd
dcGOR/man/dcAlgoPredictMain.Rd
dcGOR/man/Pfam2GOCC.Rd
dcGOR/man/Pfam2GOBP.Rd
dcGOR/man/dcDAGannotate.Rd
dcGOR/man/dcRWRpipeline.Rd
dcGOR/man/SCOP.sf2DO.Rd
dcGOR/man/SCOP.sf2GOCC.Rd
dcGOR/man/dcList2Matrix.Rd
dcGOR/man/eTOL.Rd
dcGOR/man/dcAlgo.Rd
dcGOR/man/SCOP.sf2GOBP.Rd
dcGOR/man/dcBuildInfoDataFrame.Rd
dcGOR/man/InterPro.Rd
dcGOR/man/dcTreeConnectivity.Rd
dcGOR/man/dcAlgoPropagate.Rd
dcGOR/man/dcAlgoPredictPR.Rd
dcGOR/man/Coutput-class.Rd
dcGOR/man/SCOP.fa2MP.Rd
dcGOR/man/SCOP.sf2GOMF.Rd
dcGOR/man/Onto-class.Rd
dcGOR/man/Onto-method.Rd
dcGOR/man/Rfam2GOBP.Rd
dcGOR/man/dcDAGdomainSim.Rd
dcGOR/man/Cnetwork-class.Rd
dcGOR/man/Rfam2GOMF.Rd
dcGOR/man/SCOP.fa2DO.Rd
dcGOR/man/SCOP.sf2HPPA.Rd
dcGOR/man/dcAncestralML.Rd
dcGOR/man/SCOP.fa2HPMI.Rd