3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

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Documentation for package ‘R3CPET’ version 1.14.0

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A B C D E G H I L N O P R S T U V W

R3CPET-package 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

-- A --

annotateExpression Add the gene expression attribute to the graph nodes
annotateExpression-method Add the gene expression attribute to the graph nodes
annotateExpression-methods Add the gene expression attribute to the graph nodes

-- B --

betas Class '"HLDAResult"'
betas-method Class '"HLDAResult"'
betas-methods Class '"HLDAResult"'
Biogrid Biogrid Network
buildNetworks Building interaction networks connecting interacting regions
buildNetworks-method Building interaction networks connecting interacting regions

-- C --

ChiapetExperimentData 3CPET used raw data
ChiapetExperimentData-class 3CPET used raw data
ChromMaintainers Chomatin maintainer networks
ChromMaintainers-class Chomatin maintainer networks
Chromosoms Human chromosom lenghts
chromosoms Human chromosom lenghts
cluesOrSota-class Wrapper for 'clues' and 'sota' S3 classes
clusterInteractions Grouping DNA interactions by enrichment profile
clusterInteractions-method Grouping DNA interactions by enrichment profile
CreateCenteredBED Create centered interactions
CreateCenteredBED-method Create centered interactions
CreateCenteredBED-methods Create centered interactions
createIndexes Preparing TF indexes per region
createIndexes-method Preparing TF indexes per region
createIndexes-methods Preparing TF indexes per region
createServer Explore results in a web browser
createServer-method Explore results in a web browser
createServer-methods Explore results in a web browser

-- D --

docPerTopic Class '"HLDAResult"'
docPerTopic-method Class '"HLDAResult"'
docPerTopic-methods Class '"HLDAResult"'

-- E --

EnsemblToHGNC Ensemble to HGNC conversion
EntrezToHGNC Entrez to HGNC conversion

-- G --

geneLocations Nucleus located genes
geneLocations.nucleus Nucleus located genes
GenerateGmlNetworks Chomatin maintainer networks
GenerateGmlNetworks-method Chomatin maintainer networks
GenerateGmlNetworks-methods Chomatin maintainer networks
GenerateNetworks Generate a list of 'igraph' networks
GenerateNetworks-method Generate a list of 'igraph' networks
GenerateNetworks-methods Generate a list of 'igraph' networks
getClusters Chomatin maintainer networks
getClusters-method Chomatin maintainer networks
getClusters-methods Chomatin maintainer networks
getRegionsIncluster list of interactions per cluster
getRegionsIncluster-method list of interactions per cluster
getRegionsIncluster-methods list of interactions per cluster
getRegionsInNetwork list of interactions per network
getRegionsInNetwork-method list of interactions per network
getRegionsInNetwork-methods list of interactions per network
GOEnrich.folder GO enrichment methods
GOEnrich.folder-method GO enrichment methods
GOEnrich.folder-methods GO enrichment methods
GOEnrich.networks GO enrichment methods
GOEnrich.networks-method GO enrichment methods
GOEnrich.networks-methods GO enrichment methods

-- H --

HLDAResult Class '"HLDAResult"'
HLDAResult-class Class '"HLDAResult"'
HPRD HPRD protein interaction Network

-- I --

InferNetworks Network construction using Hierarchical Dirichlet Process
InferNetworks-method Network construction using Hierarchical Dirichlet Process
InferNetworks-methods Network construction using Hierarchical Dirichlet Process

-- L --

loadPETs Parsing ChIA-PET interaction data
loadPETs-method Parsing ChIA-PET interaction data
loadPETs-methods Parsing ChIA-PET interaction data
loadPPI Setting the background protein-protein interaction
loadPPI-method Setting the background protein-protein interaction
loadPPI-methods Setting the background protein-protein interaction
loadTFBS Loading TF binding sites
loadTFBS,ChiapetExperimentData Loading TF binding sites
loadTFBS-method Loading TF binding sites
loadTFBS-methods Loading TF binding sites

-- N --

NetworkCollection protein interaction networks maintaining DNA loops
NetworkCollection-class protein interaction networks maintaining DNA loops
networks protein interaction networks maintaining DNA loops
networks-method Chomatin maintainer networks
networks-method protein interaction networks maintaining DNA loops

-- O --

outputGenesPerClusterToDir List of genes in each cluster
outputGenesPerClusterToDir-method List of genes in each cluster
outputGenesPerClusterToDir-methods List of genes in each cluster
outputGenesPerNetworkToDir List of genes controlled by each network
outputGenesPerNetworkToDir-method List of genes controlled by each network
outputGenesPerNetworkToDir-methods List of genes controlled by each network

-- P --

pet 3CPET used raw data
pet-method 3CPET used raw data
pet-methods 3CPET used raw data
pet<- 3CPET used raw data
pet<--method 3CPET used raw data
plot3CPETRes Plotting clustering results
plot3CPETRes-method Plotting clustering results
plot3CPETRes-methods Plotting clustering results
plotTrack Plot interaction on a genomic track
plotTrack-method Plot interaction on a genomic track
plotTrack-methods Plot interaction on a genomic track
ppi 3CPET used raw data
ppi-method 3CPET used raw data
ppi-methods 3CPET used raw data
PPI.Biogrid Biogrid Network
PPI.HPRD HPRD protein interaction Network
ppi<- 3CPET used raw data
ppi<--method 3CPET used raw data
PrepareData Loading the raw data all at once
PrepareData-method Loading the raw data all at once
PrepareData-methods Loading the raw data all at once

-- R --

R3CPET 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
RPKMS A gene expression dataset

-- S --

sizes protein interaction networks maintaining DNA loops
sizes-method protein interaction networks maintaining DNA loops

-- T --

TF protein interaction networks maintaining DNA loops
TF-method protein interaction networks maintaining DNA loops
tfbs 3CPET used raw data
tfbs-method 3CPET used raw data
tfbs-methods 3CPET used raw data
tfbs<- 3CPET used raw data
tfbs<--method 3CPET used raw data
topEdges Chomatin maintainer networks
topEdges-method Chomatin maintainer networks
topEdges-methods Chomatin maintainer networks
topNodes Chomatin maintainer networks
topNodes-method Chomatin maintainer networks
topNodes-methods Chomatin maintainer networks

-- U --

updateResults update top maintain networks elements
updateResults-method update top maintain networks elements
updateResults-methods update top maintain networks elements

-- V --

visualizeCircos Generate circos plot per cluster
visualizeCircos-method Generate circos plot per cluster
visualizeCircos-methods Generate circos plot per cluster
visualizeInteractions Display a Circos plot of ChIA-pet interactions
visualizeInteractions-method Display a Circos plot of ChIA-pet interactions
visualizeInteractions-methods Display a Circos plot of ChIA-pet interactions

-- W --

wordsPerTopic Class '"HLDAResult"'
wordsPerTopic-method Class '"HLDAResult"'
wordsPerTopic-methods Class '"HLDAResult"'