computeCellFrequencyDistributions: Gathering of cell frequency probability distributions

In expands: Expanding Ploidy and Allele-Frequency on Nested Subpopulations

Description

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

Usage

computeCellFrequencyDistributions(dm, max_PM=6, p, min_CF=0.1, ploidy = 2, nc = 1, v = T)

Arguments

dm	Matrix in which each row corresponds to a mutation. Has to contain at least the following column names: 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 count 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.
p	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_CF	Lower boundary for the prevalence of a mutated cell (default: 0.1).
ploidy	The background ploidy of the sequenced sample (default: 2). Changing the value of this parameter is not recommended. Dealing with cell lines or tumor biopsies of very high (>=0.95) tumor purity is a necessary but not sufficient condition to change the value of this parameter.
nc	The number of nodes to be forked to run R in parallel.
v	Give a more verbose output.

Value

List with three fields:

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.

Author(s)

Noemi Andor

expands documentation built on Sept. 5, 2021, 5:18 p.m.