GBA-centrality-C

This repository contains the C code for the GBA centrality scoring algorithm. It does the heavy lifting behind our python GBA centrality software, or can be used stand-alone.

Install GBA-centrality-C

git clone https://github.com/jedrzejkubica/GBA-centrality-C.git
cd GBA-centrality-C
make

This generates an executable testAdjacency and a shared library gbaCentrality.so.

To make sure the installation is correct, run testAdjacency, which computes and prints GBA centrality scores for four example networks.

Use GBA-centrality-C

GBA-centrality-C can be used stand-alone by calling the gbaCentrality() function in the shared library gbaCentrality.so. The function arguments are as follows (for details see gbaCentrality.h):

• pointer to a network structure defining a network (see network.h)
• pointer to a geneScores structure defining seeds (see scores.h)
• alpha attenuation parameter (0 < alpha < 1, typically 0.5 is good)
• pointer to allocated memory for another geneScores structure, the content will be filled with GBA centrality scores

Dependencies

• None for production
• For development you can install "bear", which allows to build a compilation database for LSP (usable by emacs and other IDEs). Then call make all instead of make