LEANR (version 1.4.9)

subnet.simulation: Simulate subnetworks

Description

Simulate subnetworks (also called modules) and gene p-values to be then used in a ROC performance evaluation study.

Usage

subnet.simulation(g, nmods=10, mod_lims=c(10,50), pval_scaling=0.1, mod_enrich_perc=0.5,  spec='', prob_function=function(degs){degs/sum(degs)}, create.files=T)

Arguments

g

igraph graph representing the network in which subnetworks are supposed to be simulated

nmods

number of subnetworks/modules to simulate

mod_lims

minimum and maximum size (number of genes) of each module

pval_scaling

parameter value for

mod_enrich_perc

parameter value for

spec

string, specifier appended to the created pvalue files (if create.files=T)

prob_function

probability function used for picking attachment point in iterative construction of subnetworks. defaults to preferential attachment based on node degree. To disable preferential attachment, use prob_function=function(degs)rep(1/length(degs),length(degs))

create.files

whether to write subnetwork simulation results to file so external approaches can be run and evaluated on them

Value

A list object containing the simulated subnetworks. The list encompasses the following elements: A list object containing the simulated subnetworks. The list encompasses the following elements:

References

Gwinner et al., Network-based analysis of omics data: The LEAN method, MS submitted to Bioinformatics

Examples

### See vignette("subnet-sim") for a use case.