These scores quantify the evidence for each solution contributed by explanation of the observed HSCRs as integer SCNAs. These computations are independent for each sample. The input data consist of N HSCRs xi, i ∈ {1, …, N}. Each of these is observed with standard error σi, and corresponds to a genomic fraction denoted wi. Each of the xi is assumed to have arisen from either one of Q integer copy-number states: Q = {0,1, …, Q − 1}, or an additional state Z corresponding to subclonal copy-number. We refer to the collection of possible copy-states as S = Q ∪ Z. We define Q + 1 indicators s for the copy-state of each segment, with p(si) representing the probability of segment i having been generated from state s ∈ S. The integer copy-states of S are indexed by q ∈ Q; the non-integer state is denoted by z.
