subnet.simulation: Simulate subnetworks

In fgwinner/LEANR: Finds "Local Subnetworks" Within an Interaction Network which Show Enrichment for Differentially Expressed Genes

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 <p_scale>
mod_enrich_perc	parameter value for <p_enrich>
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:

mods	List of simulated modules/subnetworks. Each module is given by the igraph indices of the nodes contained in it.
pvals	Result table containing for each gene in the graph its simulated pvalue (column P.Value) and its association to subnetworks or background (column NodeType)
pvalfile	String containing the name of the file containing the equivalent information to <pvals> created in this run if create.files=T

Author(s)

Frederik Gwinner

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.

fgwinner/LEANR documentation built on May 16, 2019, 12:51 p.m.