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CNVtools (version 1.66.0)

A package to test genetic association with CNV data

Description

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

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Version

Version

1.66.0

License

GPL-3

Maintainer

Chris Barnes

Last Published

February 15th, 2017

Functions in CNVtools (1.66.0)

CNV.fitModel

Fits a mixture of Gaussian to a set of one dimensional points.
CNVtest.qt

Fits a mixture of Gaussian to CNV data
CNVtools-package

CNVtools : CNV association studies
apply.pca

Applies to the data a principal component analysis
CNVtest.select.model

Select number of components in a CNV
cnv.plot

Plots posterior probabilty distributions
get.model.spec

Get model specifications (internal function)
test.posterior

Checks posterior probabilities are monotonic.
ExpandData

Expands a CNV input data frame for the maximum likelihood routines
getQualityScore

Computes a quality score for a CNV fit
CNVtest.binary

Fits a mixture of Gaussian to CNV data
qt.plot

Makes signal vs trait plots and posterior probabilty distributions
CNVtest.qt.T

Fits a mixture of Gaussian to CNV data
EM.starting.point

Randomly assigns a starting point for the EM algorithm
CNVtest.binary.T

CNV association testing using T distributions
compact.data.frame

Compacts the expanded data frame format needed by our fitting procedure into more compact and user friendly version
getparams

Return mixture parameters
A112

Copy Number Variant intensity data
apply.ldf

Applies a canonical correlation transformation to the data