A package to test genetic association with CNV data


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Documentation for package ‘CNVtools’ version 1.70.0

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CNVtools-package CNVtools : CNV association studies
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 points.
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 CNVtools : CNV association studies
compact.data.frame Compacts the expanded data frame format needed by our fitting procedure into more compact and user friendly version
EM.starting.point Randomly assigns a starting point for the EM algorithm
ExpandData Expands a CNV input data frame for the maximum likelihood routines
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 distributions
test.posterior Checks posterior probabilities are monotonic.