DNAcopy: A Package for Analyzing DNA Copy Data

This document presents an overview of the DNAcopy package. This package is for analyzing array DNA copy number data, which is usually (but not always) called array Comparative Genomic Hybridization (array CGH) data (Pinkel et al., 1998; Snijders et al., 2001; Lucito et al., 2003). It implements our methodology for finding change-points in these data (Olshen et al., 2004), which are points after which the (log) test over reference ratios have changed location. Our model is that the change-points correspond to positions where the underlying DNA copy number has changed. Therefore, change-points can be used to identify regions of gained and lost copy number. We also provide a function for making relevant plots of these data.