DNAcopy

Dependencies & Environment

Package-intrinsic requirements from the Bioconductor landing page, reproduce in any R environment.

• Version: 1.86.0 · Bioconductor: 3.23 · R: ≥ 4.6
• Depends: Imports
• System requirements: URL
• Install: BiocManager::install("DNAcopy")

When to Use

• Copy Number Segmentation: Finding change-points in array DNA copy number data (e.g., array CGH) using the segment() function.
• Identifying Gains and Losses: Determining regions of gained and lost copy number by plotting segment means with plot().
• Outlier Smoothing: Smoothing single point outliers in log-ratio data prior to segmentation using smooth.CNA().

When NOT to Use

• For allele-specific copy number estimation or tumor purity/ploidy correction, use PureCN because DNAcopy only segments total copy number.
• For single-cell DNA copy number profiling where specialized noise models are required, use AneuFinder because DNAcopy assumes bulk-level signal distributions.
• For multi-sample joint segmentation, use copynumber because DNAcopy processes samples independently.

Data Requirements

• Input Object: Data must be converted into a CNA object using the CNA() function.
• Required Columns: A matrix or vector of log-ratio data, a vector of Chromosome identifiers, and a vector of Position (map locations).
• Data Type: Typically specified as data.type="logratio".