# Segmentation of single- and multi-track copy number data by penalized least squares regression.

## Documentation for package ‘copynumber’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

aspcf | Allele-specific copy number segmentation.
BAF | Artificial SNP array data
callAberrations | Call aberrations in segmented data
getGRangesFormat | Get segments on the GRanges format
imputeMissing | Impute missing copy number values
interpolate.pcf | Interpolation of pcf-estimates.
logR | Artificial SNP array data
lymphoma | 3K aCGH data
micma | Subset of 244K aCGH data
multipcf | Multi-sample copy number segmentation.
pcf | Single-sample copy number segmentation.
pcfPlain | Plain single-sample copy number segmentation.
plotAberration | Plot areas with copy number aberrations
plotAllele | Plot SNP data and/or aspcf segmentation results
plotChrom | Plot copy number data and/or segmentation results by chromosome
plotCircle | Plot a circular genome with aberration frequencies and connections between genomic loci added.
plotFreq | Plot percentage of samples with an aberration at a genomic position
plotGamma | Plot segmentation results for several values of gamma
plotGenome | Plot copy number data and/or segmentation results
plotHeatmap | Plot copy number heatmap
plotSample | Plot copy number data and/or segmentation results by sample
selectSegments | Select multipcf segments
subsetData | Retrieve a data subset
subsetSegments | Retrieve a subset of segments
winsorize | Winsorization of copy number data