Creates a matching random module for each actual module.
Arguments
- pruned_modules
Data frame of pruned modules, required columns:
- regulator
Character, transcriptional regulator.
- target
Character, target gene of the transcriptional regulator (member of the regulator's pruned module).
- network_genes
Character vector of all genes in the network.
- seed
Integer, the seed to use for the random sampling (default: 42).
Value
Data frame of the random modules with the following columns:
- regulator
Character, transcriptional regulator.
- module_size
Integer, the number of genes assigned to a regulator (only present if the column is also present in the input
pruned_modules).- target
Character, member gene of the regulator's random module.
Details
The function outputs a random module for each module in pruned_modules. The random modules have the same regulators and contain the same number of target genes as the original modules, but these target genes are randomly drawn from network_genes.
In the next steps of the pipeline, the actual modules are compared to these random modules in terms of the statistics calculated to check whether the 2 groups of modules behave in general differently (see plotPresStatDistributions, plotPresStats, plotTreeStatDistributions and plotTreeStats) and to remove those individual actual modules that show too similar characteristics to the random modules (see filterModuleTrees).