FREGAT: an R package for region-based association analysis

Nadezhda M Belonogova; Gulnara R Svishcheva; Tatiana I Axenovich

doi:10.1093/bioinformatics/btw160

FREGAT: an R package for region-based association analysis

Bioinformatics. 2016 Aug 1;32(15):2392-3. doi: 10.1093/bioinformatics/btw160. Epub 2016 Mar 24.

Authors

Nadezhda M Belonogova¹, Gulnara R Svishcheva², Tatiana I Axenovich³

Affiliations

¹ Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk.
² Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk Vavilov Institute of General Genetics, the Russian Academy of Sciences, Moscow, Russia.
³ Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk Novosibirsk State University, Novosibirsk, Russia.

PMID: 27153598
DOI: 10.1093/bioinformatics/btw160

Abstract

Several approaches to the region-based association analysis of quantitative traits have recently been developed and successively applied. However, no software package has been developed that implements all of these approaches for either independent or structured samples. Here we introduce FREGAT (Family REGional Association Tests), an R package that can handle family and population samples and implements a wide range of region-based association methods including burden tests, functional linear models, and kernel machine-based regression. FREGAT can be used in genome/exome-wide region-based association studies of quantitative traits and candidate gene analysis. FREGAT offers many useful options to empower its users and increase the effectiveness and applicability of region-based association analysis.

Availability and implementation: https://cran.r-project.org/web/packages/FREGAT/index.html

Supplementary information: Supplementary data are available at Bioinformatics Online.

Contact: belon@bionet.nsc.ru.

MeSH terms

Exome*
Humans
Linear Models*
Software*