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

Documentation for package ‘copynumber’ version 1.18.0

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