Cascade (version 2.1)

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 network
cutoff(Omega, sequence = NULL, x_min = 0)

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

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.

Author

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

# \donttest{
	data(network)
	cutoff(network)
	#See vignette for more details
# }