Pre-Installed Plugins

“pvalues” plugin

This plugin performs the binomial test to determine enrichment of phenotypes of interest within the networks identified by DRIVE’s clustering algorithm. This plugin updates two attributes of the network class: “min_pvalue_str” and “pvalues”. The plugin will construct a string that has the most statistically enriched phenotype ID, the corresponding p-value, and the phenotype description if it is provided. The plugin also generates a dictionary where the keys are the phenotype IDs and the values are strings that describe the number of carriers in the network, the IDs of the carriers in the network, how many individuals are excluded from the network, and then the p-value calculated from the binomial test.

“network writer” plugin

This plugin is responsible for writing all the output about what clusters were detected and if those networks are enriched for a phenotype of interest to a file. This plugin will create a file with the extension “*drive.networks.txt”. This plugin has to be run after the p-values plugin because it uses some of the results of the p-values plugin.