About RVASSOC

RVASSOC is a simple program for performing various tests for association between genotypes and disease status using biallelic sequence variants from unrelated cases and controls. It was designed to accommodate both rare variants and missing genotypes. More specifically, it implements the Cochran-Armitage (CA) max/sum tests, the Combined Multivariate and Collapsing (CMC) test, and the Weighted Sum Statistic (WSS) test for case-control designs with independent subjects, biallelic variants, and no covariates.

RVASSOC was written and is supported by:

Daniel D. Kinnamon
Division of Human Genetics
Department of Internal Medicine
The Ohio State University Wexner Medical Center
Biomedical Research Tower, Room 384
460 W. 12th Ave.
Columbus, OH 43210
E-mail: Daniel-DOT-Kinnamon-AT-osumc-DOT-edu

License

Copyright © 2010-12 University of Miami Miller School of Medicine

RVASSOC incorporates functions from the GNU Scientific Library (GSL), which is distributed under the GNU General Public License version 3. This statement hereby explicitly incorporates all copyrights pertaining to GSL functions used in RVASSOC, which can be found in the GSL header files included in the RVASSOC source.

RVASSOC is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License version 3 as published by the Free Software Foundation.

RVASSOC is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License version 3 for more details.

Citation

RVASSOC requires two citations: one for the software and one for the statistical test used. Information that must be supplied by users in the software citation is in bold.

RVASSOC Software

Kinnamon DD. RVASSOC: Rare Variant ASSOCiation [Source code on Internet]. Version X. Miami (FL): University of Miami Miller School of Medicine; DD MMM YYYY version release date [cited DD MMM YYYY download date]. Available from: http://rvassoc.sourceforge.io.

CA Max/Sum Tests

Kinnamon DD, Hershberger RE, Martin ER. Reconsidering association testing methods using single-variant test statistics as alternatives to pooling tests for sequence data with rare variants. PLoS ONE. 2012;7(2):e30238. Epub 2012 Feb 17. PMID: 22363423.

CMC Test

Li B, Leal SM. Methods for detecting associations with rare variants for common diseases: application to analysis of sequence data. Am J Hum Genet. 2008 Sep 12;83(3):311-21. Epub 2008 Aug 7. PMID: 18691683.

WSS Test

Madsen BE, Browning SR. A groupwise association test for rare mutations using a weighted sum statistic. PLoS Genet. 2009 Feb;5(2):e1000384. Epub 2009 Feb 13. PMID: 19214210.