CNVassoc: Association Analysis of CNV Data and Imputed SNPs

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 <isubirana@imim.es>
License
GPL (>= 2)
Version
2.2
URLs

View on CRAN

Man pages

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...

Files in this package

CNVassoc
CNVassoc/inst
CNVassoc/inst/doc
CNVassoc/inst/doc/CNVassoc_vignette.Rnw
CNVassoc/inst/doc/CNVassoc_vignette.pdf
CNVassoc/inst/doc/changelog.txt
CNVassoc/inst/doc/CNVassoc_vignette.R
CNVassoc/src
CNVassoc/src/NRlogisticcov.c
CNVassoc/src/Makevars
CNVassoc/src/NRinterweibullcov.c
CNVassoc/src/NRweibullcov.c
CNVassoc/src/loglikinterweibullcov.c
CNVassoc/src/sampleC.c
CNVassoc/src/maxC.c
CNVassoc/src/NRlogistic.c
CNVassoc/src/logliklogistic.c
CNVassoc/src/CNVassoc.h
CNVassoc/src/loglikweibull.c
CNVassoc/src/dqrls.f
CNVassoc/src/NRweibull.c
CNVassoc/src/outerC.c
CNVassoc/src/logliklogisticcov.c
CNVassoc/src/NRinterlogisticcov.c
CNVassoc/src/NRinterlogistic.c
CNVassoc/src/NRinterweibull.c
CNVassoc/src/loglikinterweibull.c
CNVassoc/src/loglikinterlogisticcov.c
CNVassoc/src/init.c
CNVassoc/src/loglikinterlogistic.c
CNVassoc/src/loglikweibullcov.c
CNVassoc/src/simcensrespC.c
CNVassoc/NAMESPACE
CNVassoc/R
CNVassoc/R/plot.cnv.probabilities.R
CNVassoc/R/cnv.R
CNVassoc/R/logistic.fit.R
CNVassoc/R/logLike.weibull.R
CNVassoc/R/print.cnv.R
CNVassoc/R/mixture.R
CNVassoc/R/cnvBatches.R
CNVassoc/R/NRnorm.R
CNVassoc/R/getQualityScore.default.R
CNVassoc/R/print.anova.CNVassoc.R
CNVassoc/R/linear.fit.R
CNVassoc/R/EMpoisson.R
CNVassoc/R/logLik.survreg.R
CNVassoc/R/plot.cnv.intensities.R
CNVassoc/R/logLike.logistic.R
CNVassoc/R/logLik.CNVassoc.R
CNVassoc/R/signalPlot.R
CNVassoc/R/CNVassoc.R
CNVassoc/R/print.CNVtest.R
CNVassoc/R/plapply.R
CNVassoc/R/CNVtest.R
CNVassoc/R/simCNVdataPois.R
CNVassoc/R/NRlogistic.R
CNVassoc/R/NRpoisson.R
CNVassoc/R/getQualityScore.R
CNVassoc/R/EMWeibull.R
CNVassoc/R/hessianLogistic.R
CNVassoc/R/EMlogistic.R
CNVassoc/R/getPvalBH.R
CNVassoc/R/classCNV.R
CNVassoc/R/getProbs.cghCall.R
CNVassoc/R/fastCNVinter.R
CNVassoc/R/hessianPoisson.R
CNVassoc/R/simNormMixt.R
CNVassoc/R/print.QualityScore.R
CNVassoc/R/getProbsRegions.i.R
CNVassoc/R/logLike.norm.R
CNVassoc/R/fastCNVassoc.R
CNVassoc/R/simCNVdataWeibull.R
CNVassoc/R/plotSignal.R
CNVassoc/R/assocCNV.i.R
CNVassoc/R/simCNVdataCaseCon.R
CNVassoc/R/is.cnv.R
CNVassoc/R/matrix2vector.R
CNVassoc/R/is.quantitative.R
CNVassoc/R/multiCNVassoc.R
CNVassoc/R/EMnorm.R
CNVassoc/R/NRWeibull.R
CNVassoc/R/z[.cnv.R
CNVassoc/R/mix.R
CNVassoc/R/getProbsRegions.R
CNVassoc/R/getProbs.cnv.R
CNVassoc/R/simCNVdataBinary.R
CNVassoc/R/ifelsem.R
CNVassoc/R/plot.cnv.R
CNVassoc/R/logLike.poisson.R
CNVassoc/R/checkCNV.R
CNVassoc/R/hessianLinear.R
CNVassoc/R/subset.cnv.R
CNVassoc/R/vector2matrix.R
CNVassoc/R/hessianWeibull.R
CNVassoc/R/anova.CNVassoc.R
CNVassoc/R/print.CNVassoc.R
CNVassoc/R/cnvDefault.R
CNVassoc/R/translate.r
CNVassoc/R/firstlib.R
CNVassoc/R/poisson.fit.R
CNVassoc/R/EMmixt.R
CNVassoc/R/print.summary.CNVassoc.R
CNVassoc/R/simCNVdataNorm.R
CNVassoc/R/summary.CNVassoc.R
CNVassoc/R/weibull.fit.R
CNVassoc/R/getProbs.R
CNVassoc/R/getQualityScore.cnv.R
CNVassoc/vignettes
CNVassoc/vignettes/main_figure_new.pdf
CNVassoc/vignettes/main_fugure_Q.pdf
CNVassoc/vignettes/CNVassoc_vignette.bib
CNVassoc/vignettes/fig1.pdf
CNVassoc/vignettes/CNVassoc_vignette.Rnw
CNVassoc/MD5
CNVassoc/build
CNVassoc/build/vignette.rds
CNVassoc/DESCRIPTION
CNVassoc/man
CNVassoc/man/getProbsRegions.Rd
CNVassoc/man/plotSignal.Rd
CNVassoc/man/simCNVdataWeibull.Rd
CNVassoc/man/simCNVdataPois.Rd
CNVassoc/man/simCNVdataNorm.Rd
CNVassoc/man/CNVassoc-internal.Rd
CNVassoc/man/getQualityScore.Rd
CNVassoc/man/fastCNVinter.Rd
CNVassoc/man/getPvalBH.Rd
CNVassoc/man/CNVtest.Rd
CNVassoc/man/simCNVdataCaseCon.Rd
CNVassoc/man/fastCNVassoc.Rd
CNVassoc/man/CNVassoc.Rd
CNVassoc/man/multiCNVassoc.Rd
CNVassoc/man/cnv.Rd
CNVassoc/man/getProbs.Rd
CNVassoc/man/simCNVdataBinary.Rd