# A package to test genetic association with CNV data

## Documentation for package ‘CNVtools’ version 1.40.2

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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.