Choose the best cutoff

Allows estimating the best cutoff. For a sequence of cutoff, the p value corresponding to each cutoff value of the sequence. Mainly recommended for single time cascade networks. To achieve more sparsity in other settings, please use a fiiting function based on the stability selection or selectboost algorithms.

Usage

# S4 method for class 'omics_network'
cutoff(Omega, sequence = NULL, x_min = 0)

Arguments

Omega

a omics_network object

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

Author

Bertrand Frederic, Myriam Maumy-Bertrand.

Examples

# \donttest{
    data(network)
    cutoff(network)
#> [1] "This computation 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 0.081 0.974 0.585 0.045 0.377 0.172 0.049 0.006

#> $p.value
#>  [1] 0.000 0.000 0.081 0.974 0.585 0.045 0.377 0.172 0.049 0.006
#> 
#> $p.value.inter
#>  [1] -0.10507152  0.13978653  0.39801072  0.72456545  0.59335316  0.23310072
#>  [7]  0.22014627  0.17394550  0.09493869 -0.01411841
#> 
#> $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
# }