dmGWAS2-package: dmGWAS2: Search for dense modules in a node- and...

In aaronwolen/dmGWAS2: A fork of EW_dmGWAS

Description

dmGWAS2 constructs a node- and edge-weighted PPI network, performs dense module searching, generates simulation data from random networks, normalizes module scores using simulation data, removes unqualified modules, and orders resultant modules according to their significance.

Details

This package takes three types of data as input: a list of genes with association p-values, gene expression profiling in both case and control samples, and a human PPI network. generate_graph constructs a node- and edge-weighted PPI network. dms performs dense module search upon the node- and edge-weighted PPI network.

References

Jia P, Zheng S, Long J, Zheng W, and Zhao Z (2011) dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics 27(1):95-102.

Wang Q, Yu H, Zhao Z, and Jia P. EW_dmGWAS: Edge-weighted dense module search for genome-wide association studies and gene expression profiles. Manuscript in preparation.

aaronwolen/dmGWAS2 documentation built on May 10, 2019, 4:04 a.m.