Description Usage Arguments Value Author(s)
View source: R/computeCellFrequencyDistributions.R
Computes the probability distributions of cell frequencies, by calling cellfrequency_pdf
for each mutation separately.
1 | computeCellFrequencyDistributions(dm, max_PM=6, p, min_CF=0.1, ploidy = 2, nc = 1, v = T)
|
dm |
Matrix in which each row corresponds to a mutation. Has to contain at least the following column names: |
max_PM |
Upper threshold for the number of amplicons per mutated cell (default: 6). See also |
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. |
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. |
Noemi Andor
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