Description Usage Arguments Value Author(s) References Examples
Simulate subnetworks (also called modules) and gene p-values to be then used in a ROC performance evaluation study.
1 2 | 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)
|
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 |
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 |
Frederik Gwinner
Gwinner et al., Network-based analysis of omics data: The LEAN method, MS submitted to Bioinformatics
1 | ### See vignette("subnet-sim") for a use case.
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