expands (version 1.7.2)

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 of each mutation; PN_B - the ploidy of the B-allele in normal cells (binary variable: 1 if the mutation is a germline variant, 0 if somatic).

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

freq

The cellular frequencies for which probabilities are computed.

densities

Matrix 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.

dm

The input matrix with column $f$ updated according to the cellular frequency that best explains the observed allele frequency and copy number.