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dcGOR (version 1.0.6)

Analysis of Ontologies and Protein Domain Annotations

Description

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.

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Install

install.packages('dcGOR')

Monthly Downloads

63

Version

1.0.6

License

GPL-2

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Repository

https://github.com/hfang-bristol/dcGOR

Homepage

http://supfam.org/dcGOR

Maintainer

Last Published

July 27th, 2015

Functions in dcGOR (1.0.6)

SCOP domain superfamilies (sf).

Methods defined for S4 class Eoutput

dcAlgoPropagate

Function to propagate ontology annotations according to an input file

Function to determine the duplicated patterns from input data matrix

Function to conduct ontology enrichment analysis given a group of domains

Annotations of InterPro domains by Gene Ontology Cellular Component (GOCC).

Annotations of Rfam RNA families by Gene Ontology Cellular Component (GOCC).

Annotations of InterPro domains by Gene Ontology Molecular Function (GOMF).

Annotations of Pfam domains by Gene Ontology Cellular Component (GOCC).

Function to reconstruct ancestral discrete states using maximum parsimony algorithm

Annotations of SCOP domain superfamilies (sf) by Human Phenotype Phenotypic Abnormality (HPPA).

Function to assign (and evaluate) arguments with default values for an input function

Annotations of SCOP domain superfamilies (sf) by Mammalian Phenotype (MP).

Function to perform RWR-based ontology term predictions from input known annotations and an input graph

Function to extract a tip-induced subtree from a phylo-formatted phylogenetic tree

Gene Ontology Cellular Component (GOCC).

dcTreeConnectivity

Function to calculate the sparse connectivity matrix between parents and children from a phylo-formatted phylogenetic tree

Annotations of SCOP domain families (fa) by Human Phenotype Phenotypic Abnormality (HPPA).

Gene Ontology Molecular Function (GOMF).

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)

Annotations of SCOP domain families (fa) by Human Phenotype Mode of Inheritance (HPMI).

Annotations of Rfam RNA families by Gene Ontology Biological Process (GOBP).

dcBuildInfoDataFrame

Function to build an object of the S4 class InfoDataframe from an input file

InterPro domains (InterPro).

Methods defined for S4 class Onto

Definition for S4 class Coutput

Dnetwork-method

Methods defined for S4 class Dnetwork

Definition for S4 class Anno

Cnetwork-method

Methods defined for S4 class Cnetwork

Annotations of SCOP domain superfamilies (sf) by Gene Ontology Cellular Component (GOCC).

Annotations of SCOP domain families (fa) by Gene Ontology Molecular Function (GOMF).

Definition for S4 class Eoutput

Function to calculate pair-wise semantic similarity between domains based on a direct acyclic graph (DAG) with annotated data

Annotations of SCOP domain families (fa) by Gene Ontology Biological Process (GOBP).

Function to load dcGOR built-in RData

Function to apply dcGO algorithm to infer domain-centric ontology

Definition for VIRTUAL S4 class AdjData

Annotations of SCOP domain superfamilies (sf) by Human Phenotype ONset and clinical course (HPON).

Annotations of SCOP domain superfamilies (sf) by Gene Ontology Biological Process (GOBP).

Human Phenotype Mode of Inheritance (HPMI).

Definition for S4 class Cnetwork

Function to setup a pipeine to estimate RWR-based contact strength between samples from an input domain-sample data matrix and an input graph

Function to convert a list into a matrix containing three columns

Mammalian Phenotype (MP).

Definition for S4 class Dnetwork

Methods defined for S4 class Coutput

Function to build an object of the S4 class Anno from input files

Disease Ontology (DO).

Annotations of SCOP domain superfamilies (sf) by Human Phenotype Mode of Inheritance (HPMI).

Function to find supra-domains with better scores than their individual domains

eukaryotic Tree Of Life (eTOL)

Function to extract a subtree under a given clade from a phylo-formatted phylogenetic tree

Annotations of Pfam domains by Gene Ontology Biological Process (GOBP).

Function to create a sparse matrix for an input file with three columns

dcAlgoPredictMain

Function to predict ontology terms given an input file containing domain architectures (including individual domains)

InfoDataFrame-class

Definition for S4 class InfoDataFrame

Ancestral_domainome

Ancestral superfamily domain repertoires in Eukaryotes

Annotations of SCOP domain families (fa) by Human Phenotype ONset and clinical course (HPON).

Definition for VIRTUAL S4 class AnnoData

Function to obtain a list of features via splitting an input architecture

Function to convert an object between graph classes

Annotations of SCOP domain families (fa) by Gene Ontology Cellular Component (GOCC).

RNA families (Rfam).

Annotations of SCOP domain superfamilies (sf) by Gene Ontology Molecular Function (GOMF).

Annotations of Pfam domains by Gene Ontology Molecular Function (GOMF).

Annotations of Rfam RNA families by Gene Ontology Molecular Function (GOMF).

Methods defined for S4 class Anno

SCOP domain families (fa).

Human Phenotype Phenotypic Abnormality (HPPA).

Annotations of SCOP domain superfamilies (sf) by Disease Ontology (DO).

InfoDataFrame-method

Methods defined for S4 class InfoDataFrame

Function to generate a subgraph of a direct acyclic graph (DAG) induced by the input annotation data

Function to reconstruct ancestral discrete states using fast maximum likelihood algorithm

Function to perform naive prediction from input known annotations

Pfam domains (Pfam).

Human Phenotype ONset and clinical course (HPON).

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

Gene Ontology Biological Process (GOBP).

dcAlgoPredictPR

Function to assess the prediction performance via Precision-Recall (PR) analysis

Annotations of InterPro domains by Gene Ontology Biological Process (GOBP).

Function to visualise enrichment analysis outputs in the context of the ontology hierarchy

Annotations of SCOP domain families (fa) by Mammalian Phenotype (MP).

Function to build an object of the S4 class Onto from input files

Definition for S4 class Onto