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

## Documentation for package ‘R3CPET’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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"'