CNVtools: A package to test genetic association with CNV data

This package is meant to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies.

Author
Chris Barnes <christopher.barnes@imperial.ac.uk> and Vincent Plagnol <vincent.plagnol@cimr.cam.ac.uk>
Date of publication
None
Maintainer
Chris Barnes <christopher.barnes@imperial.ac.uk>
License
GPL-3
Version
1.68.0

View on Bioconductor

Man pages

A112
Copy Number Variant intensity data
apply.ldf
Applies a canonical correlation transformation to the data
apply.pca
Applies to the data a principal component analysis
CNV.fitModel
Fits a mixture of Gaussian to a set of one dimensional...
cnv.plot
Plots posterior probabilty distributions
CNVtest.binary
Fits a mixture of Gaussian to CNV data
CNVtest.binary.T
CNV association testing using T distributions
CNVtest.qt
Fits a mixture of Gaussian to CNV data
CNVtest.qt.T
Fits a mixture of Gaussian to CNV data
CNVtest.select.model
Select number of components in a CNV
CNVtools-package
CNVtools : CNV association studies
compact.data.frame
Compacts the expanded data frame format needed by our fitting...
EM.starting.point
Randomly assigns a starting point for the EM algorithm
ExpandData
Expands a CNV input data frame for the maximum likelihood...
get.model.spec
Get model specifications (internal function)
getparams
Return mixture parameters
getQualityScore
Computes a quality score for a CNV fit
qt.plot
Makes signal vs trait plots and posterior probabilty...
test.posterior
Checks posterior probabilities are monotonic.

Files in this package

CNVtools/DESCRIPTION
CNVtools/NAMESPACE
CNVtools/R
CNVtools/R/CNV.fitModel.R
CNVtools/R/CNVtest.binary.R
CNVtools/R/CNVtest.binary.T.R
CNVtools/R/CNVtest.qt.R
CNVtools/R/CNVtest.qt.T.R
CNVtools/R/CNVtest.select.model.R
CNVtools/R/EM.starting.point.R
CNVtools/R/ExpandData.R
CNVtools/R/apply.ldf.R
CNVtools/R/apply.pca.R
CNVtools/R/cnv.plot.R
CNVtools/R/compact.data.frame.R
CNVtools/R/get.model.spec.R
CNVtools/R/getQualityScore.R
CNVtools/R/getparams.R
CNVtools/R/qt.plot.R
CNVtools/R/test.posterior.R
CNVtools/build
CNVtools/build/vignette.rds
CNVtools/data
CNVtools/data/A112.RData
CNVtools/inst
CNVtools/inst/doc
CNVtools/inst/doc/CNVtools-vignette.R
CNVtools/inst/doc/CNVtools-vignette.Rnw
CNVtools/inst/doc/CNVtools-vignette.pdf
CNVtools/man
CNVtools/man/A112.Rd
CNVtools/man/CNV.fitModel.Rd
CNVtools/man/CNVtest.binary.Rd
CNVtools/man/CNVtest.binary.T.Rd
CNVtools/man/CNVtest.qt.Rd
CNVtools/man/CNVtest.qt.T.Rd
CNVtools/man/CNVtest.select.model.Rd
CNVtools/man/CNVtools-package.Rd
CNVtools/man/EM.starting.point.Rd
CNVtools/man/ExpandData.Rd
CNVtools/man/apply.ldf.Rd
CNVtools/man/apply.pca.Rd
CNVtools/man/cnv.plot.Rd
CNVtools/man/compact.data.frame.Rd
CNVtools/man/get.model.spec.Rd
CNVtools/man/getQualityScore.Rd
CNVtools/man/getparams.Rd
CNVtools/man/qt.plot.Rd
CNVtools/man/test.posterior.Rd
CNVtools/src
CNVtools/src/MyException.h
CNVtools/src/fitmodel.cpp
CNVtools/src/fitmodel.h
CNVtools/src/glm_test.cpp
CNVtools/src/glm_test.h
CNVtools/src/gmath.h
CNVtools/src/mla.cpp
CNVtools/src/routine.cpp
CNVtools/src/zeroin.c
CNVtools/vignettes
CNVtools/vignettes/CNVtools-vignette.Rnw