Cascade: cutoff-network-method – R documentation

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cutoff-network-method

Choose the best cutoff

Description

Allows estimating the best cutoff, in function of the scale-freeness of the network. For a sequence of cutoff, the corresponding p-value is then calculated.

Usage

## S4 method for signature 'network'
cutoff(Omega, sequence = NULL, x_min = 0)

Arguments

`Omega`	a network object
`sequence`	(optional) a vector corresponding to the sequence of cutoffs that will be tested.
`x_min`	(optional) an integer ; only values over x_min are further retained for performing the test.

Value

A list containing two objects :

`p.value`	the p values corresponding to the sequence of cutoff
`p.value.inter`	the smoothed p value vector, using the loess function

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)
	cutoff(network)
	#See vignette for more details

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