CNVassoc: Association Analysis of CNV Data and Imputed SNPs

The CNVassoc package carries out analysis of common Copy Number Variants (CNVs) and imputed Single Nucleotide Polymorphisms (SNPs) in population-based studies. It includes tools for estimating association under a series of study designs (case-control, cohort, etc), using several dependent variables (class status, censored data, counts) as response, adjusting for covariates and considering various inheritance models. Moreover, it is possible to perform epistasis studies with pairs of CNVs or imputed SNPs. It has been optimized in order to make feasible the analyses of Genome Wide Association studies (GWAs) with hundreds of thousands of genetic variants (CNVs / imputed SNPs). Also, it incorporates functions for inferring copy number (CNV genotype calling). Various classes and methods for generic functions (print, summary, plot, anova, ...) have been created to facilitate the analysis.

Version: 2.1
Depends: R (≥ 2.15.0), CNVassocData, mixdist, mclust, survival
Suggests: CGHcall, CGHregions, CNVtools, xtable, MASS, Biobase, CGHbase
Published: 2015-02-26
Author: Juan R González, Isaac Subirana
Maintainer: Isaac Subirana <isubirana at imim.es>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
URL: http://www.creal.cat/jrgonzalez/software.htm
NeedsCompilation: yes
CRAN checks: CNVassoc results

Downloads:

Reference manual: CNVassoc.pdf
Vignettes: CNVassoc
Package source: CNVassoc_2.1.tar.gz
Windows binaries: r-devel: CNVassoc_2.1.zip, r-release: CNVassoc_2.1.zip, r-oldrel: CNVassoc_2.1.zip
OS X Snow Leopard binaries: r-release: CNVassoc_2.1.tgz, r-oldrel: CNVassoc_2.1.tgz
OS X Mavericks binaries: r-release: CNVassoc_2.1.tgz
Old sources: CNVassoc archive