SageBionetworksCoex-package: Sage Bionetworks Coexpression

In Sage-Bionetworks/SageBionetworksCoex: Gene Coexpression

Description

Compute gene coexpression based on gene expression data. Output includes coexpression modules, diagnostic plots and supporting statistics. The package leverages the WGCNA package published to C-RAN by the UCLA Array Data Analysis Group, but includes parameter settings and custom functions to replicate the 'flavor' of the algorithm as executed at Sage Bionetworks. R version 2.13 or higher is required.

Details

Package:	SageBionetworksCoex
Type:	Package
Version:	0.12
Date:	2011-08-27
License:	What license is it under?
LazyLoad:	yes

The main entry point for this package is performCoexFromFiles(). Alternatively one may call performCoexpressionAnalysis(), and createDiagnosticPlots() directly, to perform the computation and generate the graphic output, respectively.

Note

This package requires the 'WGCNA' and (for graphics), 'lattice'.

Author(s)

Bruce Hoff <[e-mail]>

References

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/

Zhang, B. & Horvath, S. (2005) Statistical Applications in Genetics and Molecular Biology 4, Article 17.

Langfelder P, Zhang B, Horvath S (2007) Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut library for R. Bioinformatics 2008 24(5):719-720

http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/Rpackages/WGCNA/

Sage-Bionetworks/SageBionetworksCoex documentation built on May 9, 2019, 12:11 p.m.