Postgwas: advanced GWAS interpretation in R

PLoS One. 2013 Aug 19;8(8):e71775. doi: 10.1371/journal.pone.0071775. eCollection 2013.

Abstract

We present a comprehensive toolkit for post-processing, visualization and advanced analysis of GWAS results. In the spirit of comparable tools for gene-expression analysis, we attempt to unify and simplify several procedures that are essential for the interpretation of GWAS results. This includes the generation of advanced Manhattan and regional association plots including rare variant display as well as novel interaction network analysis tools for the investigation of systems-biology aspects. Our package supports virtually all model organisms and represents the first cohesive implementation of such tools for the popular language R. Previous software of that range is dispersed over a wide range of platforms and mostly not adaptable for custom work pipelines. We demonstrate the utility of this package by providing an example workflow on a publicly available dataset.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Epistasis, Genetic
  • Gene Regulatory Networks
  • Genome-Wide Association Study*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Molecular Sequence Annotation
  • Polymorphism, Single Nucleotide
  • Software*

Grants and funding

This work was supported by grant 01GS0841 of the National Genome Research Network (www.ngfn.de) funded by the Bundesministerium für Bildung und Forschung, Germany and by grants from the NRW/EU-Ziel2-Programm 2007–2013 “European Union, European Regional Development Fund, Investing in your Future” and the German federal state North Rhine-Westphalia. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.