Cascade (version 1.8)

cutoff: 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

cutoff(Omega,...)

Arguments

Omega

a network object

...

Optional arguments:

sequence

a vector corresponding to the sequence of cutoffs that will be tested.

x_min

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

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

# NOT RUN {
	data(network)
	cutoff(network)
	#See vignette for more details
# }