ChromMaintainers-class {R3CPET} | R Documentation

## Chomatin maintainer networks

### Description

The `ChromMaintainers` holds information about the inferred network by the method `InferNetworks`. It contains the list of inferred networks as `igraph` object, a list of edges and a list of proteins. In addition to an `HLDAResult` object that contains the final probabilities calculated by the HLDA algorithm.

### Usage

     ChromMaintainers( maintainers,topEdges,topNodes, clusRes = NULL, networks = list())

### Arguments

`maintainers` | Object of class `"HLDAResult"` that contains the HLDA results.
`topEdges` | a `"matrix"` containing the list the top edges per network.
`topNodes` | a `"matrix"` containing the list the top proteins per network.
`networks` | the list of infered networks as an `igraph` objects list
`clusRes` | Object of class `"cluesOrSota"` describing the assignment of each DNA-interaction to a chromatin-maintainer network according to their enrichment.

### Value

a `ChromMaintainers` object.

### Accesors

if `x` is a `ChromMaintainers` object the following accessors can be applied :

`networks(x)`

  gets the list of networks as `igraph` objects

`topNodes(x)`

  gets a `matrix` object that contains the list of top proteins per network

`topEdges(x)`

  gets a `matrix` object that contains the list of top proteins per network

`getClusters(x)`

  returns the clustering results of DNA-interaction into groups according to their partnership enrichment profile to the set of inferred chromatin maintainer networks.

### Methods

Many plotting and annotation methods are associated with this class.

`annotateExpression(object, RPKMS)`

  To add the gene expression attribute to the `igraph` objects

`clusterInteractions(object, method, nbClus )`

  To cluster the DNA-interactions according to their partnership enrichment profile.

`GenerateGmlNetworks(object,...)`

  Creates the list of `igraph` object from the `topEdges` matrix

`outputGenesPerClusterToDir(hdaRes,data,path, ...)`

  get the list genes belonging to each DNA-interaction cluster.

`getRegionsIncluster(hdaRes,data, cluster, ...)`

  returns the coordinates of the DNA interactions for a given cluster.

`GOEnrich.networks(object, pval=0.05, GOlimit= 5,path="")`

  do a `GO` enrichment of the elements of each inferred network.

`plot3CPETRes(object, path, W, H, type,byEdge, netPerRow, layoutfct, ...)`

  provide different type of plots to visualize the results

`visualizeCircos(object, data, cluster, chrLenghts)`

  Draws a circos plot of the DNA interactions in a given cluster.

### Author(s)

Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)

### References

https://www.cs.princeton.edu/~blei/topicmodeling.html (C. Wang's hdp code)

Chong Wang, John Paisley and David M. Blei, Online variational inference for the hierarchical Dirichlet process .In AISTATS 2011

Mohamed Nadhir D, Yang C et al 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process, ....

### See Also

`InferNetworks`, `ChromMaintainers` , `HLDAResult`

### Examples

    showClass("ChromMaintainers")

[Package R3CPET version 1.18.0 Index]