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.
||R (≥ 2.15.0), CNVassocData, mixdist, mclust, survival
||CGHcall, CGHregions, CNVtools, xtable, MASS, Biobase, CGHbase
||Juan R González, Isaac Subirana
||Isaac Subirana <isubirana at imim.es>
||GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]