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

Functions

anova.CNVassoc Man page
assocCGH.i Man page
bicMix Man page
cnv Man page
CNVassoc Man page
CNVassoc-internal Man page
cnvBatches Man page
cnvDefault Man page
CNVtest Man page
EMlogistic Man page
EMnorm Man page
fastCNVassoc Man page
fastCNVinter Man page
getProbs Man page
getProbs.cghCall Man page
getProbs.cnv Man page
getProbsRegions Man page
getPvalBH Man page
getQualityScore Man page
getQualityScore.cnv Man page
getQualityScore.default Man page
hessianLinear Man page
hessianLogistic Man page
is.cnv Man page
is.quantitative Man page
linear.fit Man page
logistic.fit Man page
logLik.CNVassoc Man page
matrix2vector Man page
mix Man page
mixture Man page
multiCNVassoc Man page
NRlogistic Man page
NRnorm Man page
plapply Man page
plot.cnv Man page
plot.cnv.intensities Man page
plot.cnv.probabilities Man page
plotSignal Man page
print.anova.CNVassoc Man page
print.cnv Man page
print.CNVassoc Man page
print.CNVtest Man page
print.QualityScore Man page
print.summary.CNVassoc Man page
simCNVdataBinary Man page
simCNVdataCaseCon Man page
simCNVdataNorm Man page
simCNVdataPois Man page
simCNVdataWeibull Man page
summary.CNVassoc Man page
vector2matrix Man page

Files

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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