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.

AuthorJuan R Gonzlez, Isaac Subirana
Date of publication2016-04-12 17:01:26
MaintainerIsaac Subirana <isubirana@imim.es>
LicenseGPL (>= 2)
Version2.2
http://www.creal.cat/jrgonzalez/software.htm

View on CRAN

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

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