epc {centiserve}R Documentation

Find the edge percolated component (EPC) in a graph

Description

For a node vv in G, EPC(v)EPC(v) is defined as:

EPC(v)=1vk=11000teδvtkEPC(v)=\frac{1}{\left|v\right|}\sum_{k=1}^{1000}\sum_{t\in e}\delta_{vt}^{k}

Given a threshold (0thethreshold1)(0 \leq the threshold \leq 1), we create 1000 reduced network by asigning a random number between 0 and 1 to every edge and remove edges if their associated random numbers are less than the threshold.
Let the GkG_{k} be the reduced network generated at the kthk_{th} time reduced process. If nodes uu and vv are connected in GkG_{k}, set δvtk\delta_{vt}^{k} to 1; otherwise δvtk=0\delta_{vt}^{k}=0.

Usage

epc(graph, vids = V(graph), threshold = 0.5)

Arguments

graph

The input graph as igraph object

vids

Vertex sequence, the vertices for which the centrality values are returned. Default is all vertices.

threshold

The threshold parameter, for filter graph and create reduced one, which must be between 0 and 1. The default is 0.5.

Details

For an interaction network G, assign a removing probability p to every edge. Let G'be a realization of the random edge removing from G. If nodes vv and ww are connected in G', set dvwd_{vw} be 1, otherwise set dvwd_{vw} be 0. The percolated connectivity of vv and ww, cvwc_{vw}, is defined to be the average of dvwd_{vw} over realizations. The size of percolated component containing node vv, svs_{v}, is defined to be the sum of cvwc_{vw} over nodes ww. The score of node vv, EPC(v)EPC(v), is defined to be svs_{v}.
More detail at EPC-Edge Percolated Component

Value

A numeric vector contaning the centrality scores for the selected vertices.

Author(s)

Mahdi Jalili m_jalili@farabi.tums.ac.ir

References

Lin, Chung-Yen, et al. "Hubba: hub objects analyzer-a framework of interactome hubs identification for network biology." Nucleic acids research 36.suppl 2 (2008): W438-W443.

Chen, Shu-Hwa, et al. "cyto-Hubba: A Cytoscape plug-in for hub object analysis in network biology." 20th International Conference on Genome Informatics. 2009.

Examples

g <- graph(c(1,2,2,3,3,4,4,2))
epc(g)

[Package centiserve version 1.0.0 Index]