best_subnets: The best subnetworks

In Corbi: Collection of Rudimentary Bioinformatics Tools

The best subnetworks

Description

Search best subnetworks that maximize given objective functions.

Usage

best_subnets(
  func,
  net.matrix,
  max.size = 10,
  exhaust.size = 5,
  max.top = 10000
)

Arguments

func	The objective function to maximize
net.matrix	The adjacent matrix of network
max.size	The maximal size of subnetworks
exhaust.size	The maximal size of subnetworks that use exhaustive searching strategy
max.top	The maiximal number of top candidates kept for evaluation of next size, used in heuristic searching strategy

Details

Enumerate and search the best subnetworks that maximize given objective function. If the size of subnetworks <= exhaust.size, exact exhaustive searching is applied, otherwise, heuristic searching algorithm is used.

Value

A list with the following two components:

subnets	The list of top subnetworks in different sizes
obj.values	The list of objective values of corresponding subnetworks

See Also

get_subnets, extend_subnets

Examples

library(Corbi)
net <- matrix(FALSE, nrow=10, ncol=10)
net[sample.int(100, 20)] <- TRUE
net <- net | t(net)
func <- function(subnet) max(subnet) - min(subnet)
result <- best_subnets(func, net, 5)

Corbi documentation built on May 30, 2022, 5:06 p.m.