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.
|Author||Juan R Gonzlez, Isaac Subirana|
|Date of publication||2016-04-12 17:01:26|
|Maintainer||Isaac Subirana <email@example.com>|
|License||GPL (>= 2)|
cnv: CNV object
CNVassoc: Association analysis between a CNV and phenotype
CNVassoc-internal: Internal CNVassoc functions
CNVtest: Testing association between a CNV and phenotype
fastCNVassoc: Fast association analysis between a CNV or imputed SNPs and...
fastCNVinter: Fast epistasis (pairwise interaction) analysis between two...
getProbs: Get posterior probabilities from an object of class 'cnv' or...
getProbsRegions: Get posterior probabilities for blocks/regions
getPvalBH: Corrected p values using Benjamini & Hochberg approach
getQualityScore: Computes a quality score for a CNV fit
multiCNVassoc: Association between several CNVs and disease
plotSignal: plots the intensities of a CNV univariate signal data
simCNVdataBinary: Simulation of CNV and discrete traits
simCNVdataCaseCon: Simulation of CNV in a case-control study design
simCNVdataNorm: Simulation of CNV and quantitative traits
simCNVdataPois: Simulate Poisson data
simCNVdataWeibull: Simulate of CNV and a right censored Weibull distributed...