expands (version 1.5)

computeCellFrequencyDistributions: Gathering of cell frequency probability distributions

Description

Computes the probability distributions of cell frequencies, by calling cellfrequency_pdf for each mutation separately.

Usage

computeCellFrequencyDistributions(dm, max_PM=6, precision, min_CellFreq=0.1)

Arguments

dm

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 trigger a higher number of predicted subpopulations (recommended: 0.1/log(n/7), where n=# mutations).

min_CellFreq

Lower threshold for the prevalence of a mutated cell (default: 0.1); mutations for which allele frequency x copy number are below this value, are excluded from further computation. Decreasing the value of this variable is not recommended unless extensive

Value

• List with three fields:
• freq
  The cellular frequencies for which probabilities are computed.
• densities
  Matrix 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 $freq[j].$
• dm
  The input matrix with column $f$ updated according to the cellular frequency that best explains the observed allele frequency and ploidities $(PM, PN, PN_B)$.