Algorithm optimization for weighted gene co-expression network analysis: accelerating the calculation of Topology Overlap Matrices with OpenMP and SQLite

Motivation: Weighted gene co-expression network analysis (WGCNA) is an R package that can search highly related gene modules. The most time-consuming step of the whole analysis is to calculate the Topological Overlap Matrix (TOM) from the Adjacency Matrix in a single thread. This study changes it to multithreading. Results: This paper uses SQLite for multi-threaded data transfer between R and C++, uses OpenMP to enable multi-threading and calculates the TOM via an adjacency matrix on a Shared-memory MultiProcessor (SMP) system, where the calculation time decreases as the number of physical CPU cores increases. Availability and implementation: The source code is available at https://github.com/do-somethings-haha/fast_calculate_TOM_of_WGCNA Contact: chenxin@cdutcm.edu.cn