Matrix in which each row corrsponds to a mutation. Has to contain at least the following columnnames:
chr - the chromosome on which each mutation is located;
startpos - the position of each mutation;
AF_Tumor - the allele-frequency
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 lead to a higher number of predicted subpopulations.
min_CellFreq
Lower boundary for the prevalence of a mutated cell (default: 0.1).
Value
List with three fields:
freqThe cellular frequencies for which probabilities are computed.
densitiesMatrix in which each row corresponds to a point 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 $freq[j]$ of cells.
dmThe input matrix with column $f$ updated according to the cellular frequency that best explains the observed allele frequency and copy number.