CNVassoc: Association Analysis of CNV Data and Imputed SNPs
Version 2.2

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.

Browse man pages Browse package API and functions Browse package files

AuthorJuan R Gonzlez, Isaac Subirana
Date of publication2016-04-12 17:01:26
MaintainerIsaac Subirana <isubirana@imim.es>
LicenseGPL (>= 2)
Version2.2
URL http://www.creal.cat/jrgonzalez/software.htm
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("CNVassoc")

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...

Functions

CNVassoc Man page Source code
CNVassoc-internal Man page
CNVtest Man page Source code
EMWeibull Source code
EMlogistic Man page Source code
EMmixt Source code
EMnorm Man page Source code
EMpoisson Source code
NRWeibull Source code
NRlogistic Man page Source code
NRnorm Man page Source code
NRpoisson Source code
anova.CNVassoc Man page Source code
assocCGH.i Man page
assocCNV.i Source code
bicMix Man page
checkCNV Source code
classCNV Source code
cnv Man page Source code
cnvBatches Man page Source code
cnvDefault Man page Source code
fastCNVassoc Man page Source code
fastCNVinter Man page Source code
getProbs Man page Source code
getProbs.cghCall Man page Source code
getProbs.cnv Man page Source code
getProbsRegions Man page Source code
getProbsRegions.i Source code
getPvalBH Man page Source code
getQualityScore Man page Source code
getQualityScore.cnv Man page Source code
getQualityScore.default Man page Source code
hessianLinear Man page Source code
hessianLogistic Man page Source code
hessianPoisson Source code
hessianWeibull Source code
ifelsem Source code
is.cnv Man page Source code
is.quantitative Man page
linear.fit Man page Source code
logLik.CNVassoc Man page Source code
logLik.survreg Source code
logLike.logistic Source code
logLike.norm Source code
logLike.poisson Source code
logLike.weibull Source code
logistic.fit Man page Source code
matrix2vector Man page Source code
mix Man page Source code
mixture Man page Source code
multiCNVassoc Man page Source code
onLoad Source code
onUnload Source code
plapply Man page Source code
plot.cnv Man page Source code
plot.cnv.intensities Man page Source code
plot.cnv.probabilities Man page Source code
plotSignal Man page Source code Source code
poisson.fit Source code
print.CNVassoc Man page Source code
print.CNVtest Man page Source code
print.QualityScore Man page Source code
print.anova.CNVassoc Man page Source code
print.cnv Man page Source code
print.summary.CNVassoc Man page Source code
simCNVdataBinary Man page Source code
simCNVdataCaseCon Man page Source code
simCNVdataNorm Man page Source code
simCNVdataPois Man page Source code
simCNVdataWeibull Man page Source code
simNormMixt Source code
subset.cnv Source code
summary.CNVassoc Man page Source code
translate Source code
vector2matrix Man page Source code
weibull.fit Source code

Files

inst
inst/doc
inst/doc/CNVassoc_vignette.Rnw
inst/doc/CNVassoc_vignette.pdf
inst/doc/changelog.txt
inst/doc/CNVassoc_vignette.R
src
src/NRlogisticcov.c
src/Makevars
src/NRinterweibullcov.c
src/NRweibullcov.c
src/loglikinterweibullcov.c
src/sampleC.c
src/maxC.c
src/NRlogistic.c
src/logliklogistic.c
src/CNVassoc.h
src/loglikweibull.c
src/dqrls.f
src/NRweibull.c
src/outerC.c
src/logliklogisticcov.c
src/NRinterlogisticcov.c
src/NRinterlogistic.c
src/NRinterweibull.c
src/loglikinterweibull.c
src/loglikinterlogisticcov.c
src/init.c
src/loglikinterlogistic.c
src/loglikweibullcov.c
src/simcensrespC.c
NAMESPACE
R
R/plot.cnv.probabilities.R
R/cnv.R
R/logistic.fit.R
R/logLike.weibull.R
R/print.cnv.R
R/mixture.R
R/cnvBatches.R
R/NRnorm.R
R/getQualityScore.default.R
R/print.anova.CNVassoc.R
R/linear.fit.R
R/EMpoisson.R
R/logLik.survreg.R
R/plot.cnv.intensities.R
R/logLike.logistic.R
R/logLik.CNVassoc.R
R/signalPlot.R
R/CNVassoc.R
R/print.CNVtest.R
R/plapply.R
R/CNVtest.R
R/simCNVdataPois.R
R/NRlogistic.R
R/NRpoisson.R
R/getQualityScore.R
R/EMWeibull.R
R/hessianLogistic.R
R/EMlogistic.R
R/getPvalBH.R
R/classCNV.R
R/getProbs.cghCall.R
R/fastCNVinter.R
R/hessianPoisson.R
R/simNormMixt.R
R/print.QualityScore.R
R/getProbsRegions.i.R
R/logLike.norm.R
R/fastCNVassoc.R
R/simCNVdataWeibull.R
R/plotSignal.R
R/assocCNV.i.R
R/simCNVdataCaseCon.R
R/is.cnv.R
R/matrix2vector.R
R/is.quantitative.R
R/multiCNVassoc.R
R/EMnorm.R
R/NRWeibull.R
R/z[.cnv.R
R/mix.R
R/getProbsRegions.R
R/getProbs.cnv.R
R/simCNVdataBinary.R
R/ifelsem.R
R/plot.cnv.R
R/logLike.poisson.R
R/checkCNV.R
R/hessianLinear.R
R/subset.cnv.R
R/vector2matrix.R
R/hessianWeibull.R
R/anova.CNVassoc.R
R/print.CNVassoc.R
R/cnvDefault.R
R/translate.r
R/firstlib.R
R/poisson.fit.R
R/EMmixt.R
R/print.summary.CNVassoc.R
R/simCNVdataNorm.R
R/summary.CNVassoc.R
R/weibull.fit.R
R/getProbs.R
R/getQualityScore.cnv.R
vignettes
vignettes/main_figure_new.pdf
vignettes/main_fugure_Q.pdf
vignettes/CNVassoc_vignette.bib
vignettes/fig1.pdf
vignettes/CNVassoc_vignette.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/getProbsRegions.Rd
man/plotSignal.Rd
man/simCNVdataWeibull.Rd
man/simCNVdataPois.Rd
man/simCNVdataNorm.Rd
man/CNVassoc-internal.Rd
man/getQualityScore.Rd
man/fastCNVinter.Rd
man/getPvalBH.Rd
man/CNVtest.Rd
man/simCNVdataCaseCon.Rd
man/fastCNVassoc.Rd
man/CNVassoc.Rd
man/multiCNVassoc.Rd
man/cnv.Rd
man/getProbs.Rd
man/simCNVdataBinary.Rd
CNVassoc documentation built on May 19, 2017, 11:12 p.m.