# Create Copy-Number Plots using karyoploteR functionality

## Documentation for package ‘CopyNumberPlots’ version 1.9.5

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

## Help Pages

colByCopyNumber | colByCopyNumber
computeHclustPlotOrder | computeHclustPlotOrder
EnsemblStyle | EnsemblStyle
getBAFColumn | getBAFColumn
getChrColumn | getChrColumn
getColumn | getColumn
getCopyNumberColors | getCopyNumberColors
getCopyNumberColumn | getCopyNumberColumn
getEndColumn | getEndColumn
getIDColumn | getIDColumn
getLOHColumn | getLOHColumn
getLRRColumn | getLRRColumn
getPosColumn | getPosColumn
getSegmentValueColumn | getSegmentValueColumn
getStartColumn | getStartColumn
loadCopyNumberCalls | loadCopyNumberCalls
loadCopyNumberCallsCnmops | loadCopyNumberCallsCnmops
loadCopyNumberCallsCNVkit | loadCopyNumberCallsCNVkit
loadCopyNumberCallsDECoN | loadCopyNumberCallsDECoN
loadCopyNumberCallsDNAcopy | loadCopyNumberCallsDNAcopy
loadCopyNumberCallsPanelcnmops | loadCopyNumberCallsPanelcnmops
loadCopyNumberCallspennCNV | loadCopyNumberCallspennCNV
loadCopyNumberCallsSeg | loadCopyNumberCallsSeg
loadSNPData | loadSNPData
loadSNPDataDNAcopy | loadSNPDataDNAcopy
loadSNPDataFromVCF | loadSNPDataFromVCF
plotBAF | plotBAF
plotCopyNumberCalls | plotCopyNumberCalls
plotCopyNumberCallsAsLines | plotCopyNumberCallsAsLines
plotCopyNumberSummary | plotCopyNumberSummary
plotLRR | plotLRR
plotSingleCellCopyNumberCalls | plotSingleCellCopyNumberCalls
plotSingleCellCopyNumberSummary | plotSingleCellCopyNumberSummary
prepareLabels | prepareLabels
readHDF5Ztree | readHDF5Ztree
removeNAs | removeNAs
transformChr | transformChr
UCSCStyle | UCSCStyle
Ztree2Hclust | Ztree2Hclust