Skip to contents

Generate reciprocal best hits based on set similarities

rs_rbh_sets.Rd

This function takes a nested list that contains gene modules/ sets derived from various methods and generate identifies reciprocal best hits between gene modules/sets across the different origins. WARNING! Incorrect use can cause kernel crashes. Wrapper around the Rust functions with type checks are provided in the package.

Usage

rs_rbh_sets(module_list, overlap_coefficient, min_similarity)

Arguments

module_list

A nested named list. The outer list should contain the origin of the gene modules, the inner list the names of the gene modules and the respective genes in them.

overlap_coefficient

Shall the overlap coefficient instead of the Jaccard similarity be used.

min_similarity

Minimum similarity that should exist between any two given gene modules to actually calculate RBH pairs.

Value

A list containing:

  • origin - The name of the origin of the gene modules.

  • target - The name of the target of the gene modules.

  • comparisons - Integer vector indicating how many RBH hits were identified in this comparison

  • origin_modules - Names of the gene modules from the origin.

  • target_modules - Names of the gene modules from the target.

  • similarity - The similarities between the two respective gene modules.