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.

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

data(network) cutoff(network)
#> [1] "This calculation may be long" #> [1] "1/10" #> [1] "2/10" #> [1] "3/10" #> [1] "4/10" #> [1] "5/10" #> [1] "6/10" #> [1] "7/10" #> [1] "8/10" #> [1] "9/10" #> [1] "10/10" #> [1] 0.000 0.000 0.586 0.280 0.296 0.167 0.007 0.380 0.361 0.115
#> $p.value #> [1] 0.000 0.000 0.586 0.280 0.296 0.167 0.007 0.380 0.361 0.115 #> #> $p.value.inter #> [1] -0.06406097 0.20282417 0.35238047 0.41001534 0.25106311 0.13219518 #> [7] 0.12216528 0.25027490 0.25857893 0.17835107 #> #> $sequence #> [1] 0.00000000 0.04444444 0.08888889 0.13333333 0.17777778 0.22222222 #> [7] 0.26666667 0.31111111 0.35555556 0.40000000 #>
#See vignette for more details