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CNVassoc (version 2.2)

Association Analysis of CNV Data and Imputed SNPs

Description

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.

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Version

Install

install.packages('CNVassoc')

Monthly Downloads

102

Version

2.2

License

GPL (>= 2)

Maintainer

Last Published

April 12th, 2016

Functions in CNVassoc (2.2)

getQualityScore

Computes a quality score for a CNV fit
simCNVdataWeibull

Simulate of CNV and a right censored Weibull distributed trait
getProbsRegions

Get posterior probabilities for blocks/regions
multiCNVassoc

Association between several CNVs and disease
fastCNVinter

Fast epistasis (pairwise interaction) analysis between two CNV or imputed SNPs for case-control and cohort GWA studies.
plotSignal

plots the intensities of a CNV univariate signal data
simCNVdataCaseCon

Simulation of CNV in a case-control study design
getProbs

Get posterior probabilities from an object of class 'cnv' or 'CGHcall'
getPvalBH

Corrected p values using Benjamini & Hochberg approach
cnv

CNV object
simCNVdataBinary

Simulation of CNV and discrete traits
fastCNVassoc

Fast association analysis between a CNV or imputed SNPs and phenotype for case-control and cohort GWA studies.
simCNVdataPois

Simulate Poisson data
CNVassoc

Association analysis between a CNV and phenotype
CNVtest

Testing association between a CNV and phenotype
CNVassoc-internal

Internal CNVassoc functions
simCNVdataNorm

Simulation of CNV and quantitative traits