ChromMaintainers-class: Chomatin maintainer networks

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

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 ([e-mail])

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")

R3CPET documentation built on Nov. 8, 2020, 8:05 p.m.