Bayesian network feature finder (BANFF): an R package for gene network feature selection.

ABSTRACT:

Motivation

Network marker selection on genome-scale networks plays an important role in the understanding of biological mechanisms and disease pathologies. Recently, a Bayesian nonparametric mixture model has been developed and successfully applied for selecting genes and gene sub-networks. Hence, extending this method to a unified approach for network-based feature selection on general large-scale networks and creating an easy-to-use software package is on demand.

Results

We extended the method and developed an R package, the Bayesian network feature finder (BANFF), providing a package of posterior inference, model comparison and graphical illustration of model fitting. The model was extended to a more general form, and a parallel computing algorithm for the Markov chain Monte Carlo -based posterior inference and an expectation maximization-based algorithm for posterior approximation were added. Based on simulation studies, we demonstrate the use of BANFF on analyzing gene expression on a protein-protein interaction network.

Availability

https://cran.r-project.org/web/packages/BANFF/index.html CONTACT: [e-mail], [e-mail] information: Supplementary data are available at Bioinformatics online.

SUBMITTER: Lan Z 

PROVIDER: S-EPMC5181536 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature