Description Usage Arguments Details Value Author(s) References
View source: R/clusterCellFrequencies.R
Calculates overrepresented cell frequencies using a two-step approach. Based on the assumption that passenger mutations occur within a cell prior to the driver event that initiates the expansion, each clonal expansion should be marked by multiple mutations. Thus mutations and copy number variations that took place in a cell prior to a clonal expansion should be present in a similar fraction of cells and leave a similar "frequency-trace" during their propagation.
1 | clusterCellFrequencies(densities, p, nrep=30, min_CF=0.1, verbose = T)
|
densities |
Matrix as obtained by |
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. |
nrep |
Positive integer indicating the number of algorithm repetitions (default: 30). |
min_CF |
Lower threshold for the prevalence of a mutated cell (default: 0.1). |
verbose |
Give a more verbose output. |
In the first step, mutations with similar cellular frequencies are grouped together by hierarchical cluster analysis of the probability distributions using the Kullback-Leibler divergence as a distance measure. The cell frequency at each cluster-maxima denotes the size of the subpopulation that harbors the clustered mutations. In the second step, each cluster is extended by members with similar distributions in an interval around the cluster-maxima.
SPs |
Matrix of predicted subpopulations. Each row corresponds to a subpopulation and each column contains information about that subpopulation, such as the size in the sequenced tumor bulk (column Mean Weighted) and the noise score at which the subpopulation has been detected (column score: lower values ~ higher subpopulation detection confidence). |
Noemi Andor
Noemi Andor, Julie Harness, Sabine Mueller, Hans Werner Mewes and Claudia Petritsch. (2013) ExPANdS: Expanding Ploidy and Allele Frequency on Nested Subpopulations. Bioinformatics.
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