Prune modules based on the regulator-target adjacencies by keeping a fixed number of top targets
Source:R/pruneModules.R
pruneModules_topN.RdPrunes the initial modules by keeping a fixed number of targets per transcriptional regulator with the highest regulator-target adjacencies.
Arguments
- initial_modules
Data frame of initial modules, required columns:
- regulator
Character, transcriptional regulator.
- target
Character, member gene of the regulator's initial module.
- weight
Numeric, consensus edge weight/adjacency, the weighted mean of replicate-wise edge weights.
- N
Either an integer specifying a single desired pruned module size for all modules or a named integer vector specifying the desired pruned module size for each regulator (default: 50).
Value
Data frame of the pruned modules with the following columns:
- regulator
Character, transcriptional regulator.
- module_size
Integer, the numer of genes assigned to a regulator.
- target
Character, target gene of the transcriptional regulator (member of the regulator's pruned module).
- weight
Numeric, consensus edge weight/adjacency, the weighted mean of replicate-wise edge weights.
Additional columns present in initial_modules will also be preserved in pruned_modules.
Details
Each pruned module output by the function contains the regulator and its N best target genes. When choosing the best targets, the genes are ranked based on how strongly they are connected to the regulator (regulator-target edge weight/adjacency).
Based on prior biological knowledge, N can be set to a different value for different regulators, however, in most cases it will just be the same desired module size for all modules. Fixing the sizes of all modules to the same number is a simple but widespread approach.
The modules are allowed to overlap, and in addition to having its own module, a regulator can be assigned to another regulator's module as well, in line with the notion that genes can be multifunctional and gene regulation can be combinatorial.
See also
Other methods to prune modules:
pruneModules_UIK_adj(),
pruneModules_UIK_adj_kIM()