Matrix in which each row corrsponds to a mutation. Has to contain at least the following columnnames:
chr - the chrmosome on which each mutation is located;
startpos - the position of each mutation;
AF_Tumor - the allele-frequency o
max_PM
Upper threshold for the number of amplicons per mutated cell (default: 6). See also cellfrequency_pdf.
precision
Precision with which subpopulation size is predicted, a small value reflects a high resolution and can trigger a higher number of predicted subpopulations (recommended: 0.1/log(n/7), where n=# mutations).
Value
List with three fields:
freqThe cellular frequencies for which probabilities are computed.
densitiesMatrix in which each row corresponds to a mutation and each column corresponds to a cellular frequency. Each value $densities[i,j]$represents the probability that mutation $i$ is present in a fraction $f$ of cells, where $f$ is $freq[j].$
dmThe input matrix with column $f$ updated according to the cellular frequency that best explains the observed allele frequency and ploidities $(PM, PN, PN_B)$.