Analysis of Ontologies and Protein Domain Annotations

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Documentation for package ‘dcGOR’ version 1.0.6

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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