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R
Cascade

analyze_network-network-method

Analysing the network

Description

Calculates some indicators for each node in the network.

Usage

## S4 method for signature 'network'
analyze_network(Omega, nv, label_v = NULL)

Arguments

Omega

a network object
nv

the level of cutoff at which the analysis should be done
label_v

(optionnal) the name of the genes

Value

A matrix containing, for each node, its betweenness,its degree, its output, its closeness.

Author(s)

Nicolas Jung, Frédéric Bertrand , Myriam Maumy-Bertrand.

References

Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014). Cascade: a R-package to study, predict and simulate the diffusion of a signal through a temporal gene network. Bioinformatics, btt705.

Vallat, L., Kemper, C. A., Jung, N., Maumy-Bertrand, M., Bertrand, F., Meyer, N., ... & Bahram, S. (2013). Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia. Proceedings of the National Academy of Sciences, 110(2), 459-464.

Examples

data(network)
	analyze_network(network,nv=0)
Cascade

Selection, Reverse-Engineering and Prediction in Cascade Networks

v2.0
GPL (>= 2)
Authors
Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>), Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>), Laurent Vallat [ctb], Nicolas Jung [ctb]
Initial release
2021-03-18

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