In order to facilitate rapid analysis of many cancer samples used in this study, ABSOLUTE was programed to automatically identify copy profiles that cannot be reliably called and to classify them into informative failure categories (Fig. 3a), which were defined by the following criteria. Define m̂ as the sorted vector of posterior genome-wide copy-state allocations (θ̂), so that m̂1 represents the greatest element of θ̂ (the modal copy-state). This vector was constructed with θ0 replaced by 0 if θ0 < 0.01 and b < 0.15, so that germline copy-number variants (CNVs) or regions of inherited homozygosity are not confused with small SCNAs implying very pure samples. The categories are then: non-aberrant: m̂3 < 0.001, m̂2 < 0.005, σ̂H < 0.02insufficient purity: m̂3 < 0.001, m̂2 < 0.005, σ̂H ≥ 0.02polygenomic: θ̂z > 0.2.
