Modularity
The modularity command calculates the fragmentation, heterogeneity, and modularity of the groups.
Usage: DBRetina modularity [OPTIONS]
Compute the modularity of gene sets
Options:
-i, --index-prefix TEXT Index file prefix [required]
-p, --pairwise PATH pairwise TSV file [required]
-c, --cutoff FLOAT RANGE containment cutoff [0<=x<=100; required]
-o, --output TEXT output file prefix [required]
--help Show this message and exit.
Command arguments
-i, --index-prefix TEXT Index file prefix [required]
This is the user-defined prefix that was used in the indexing step as an output prefix.
-p, --pairwise PATH the pairwise TSV file [required]
The original or a filtered pairwise TSV file.
-c, --cutoff FLOAT RANGE containment cutoff [0<=x<=100; required]
The -c --cutoff argument uses the Containment metric.
-o, --output TEXT output prefix [required]
The output files prefix.
Output files format
{output_prefix}_modularity.txt
A TSV file that provides information about the fragmentation, heterogeneity, and modularity of the groups. The TSV columns are defined as follows:
| group_name | The group name (node name) |
| fragmentation | Number of outbound edges from the node (-ve value) |
| heterogeneity | Number of inbound edges to the node |
| modularity | absolute(modularity + heterogeneity) |
The higher modularity (low value) indicates a more modular group. Which means that the group is more likely to be a representative group.
Created: July 8, 2023