FUNCTION_DESCRIPTION
findClones(m, prob = 0.95, coverage = 0.8, mode.size = 10, clone.size = 3, by = "chr", bySampling = FALSE, nsamp = 2000, force.tries = FALSE, verbose = FALSE, ...)
| m | a matrix of genes X cells (variables X observations) containing CNA values. |
|---|---|
| prob | a numeric value >= 0 and <= 1; the minimum posterior probability required for an observation to be assigned to a mode. Default: 0.95 |
| coverage | the fraction of observations that must have a posterior probability higher than <prob> to one of two modes in order for the distribution to qualify as bimodal. Default: 0.8 |
| mode.size | the minimum number of observations required to define a mode. Default: 10 |
| clone.size | the minimum number of cells required to define a clone. Default: 3 |
| by | PARAM_DESCRIPTION, Default: 'chr' |
#>#># malignant cells only cna = cna[, !colnames(cna) %in% unlist(refCells)] findClones(cna, by = 'chr')#> EM converged in 8 iterations (with relative change=3.26711e-13)#>#> EM converged in 18 iterations (with relative change=5.59294e-15)#>#> EM converged in 6 iterations (with relative change=9.07067e-12)#>#> EM converged in 20 iterations (with relative change=1.11559e-14)#>#> EM converged in 5 iterations (with relative change=5.38372e-12)#>#> EM converged in 7 iterations (with relative change=5.58664e-15)#>#> EM converged in 29 iterations (with relative change=2.61778e-12)#>#> EM converged in 2 iterations (with relative change=4.35461e-11)#>#> EM converged in 7 iterations (with relative change=0)#>#> EM converged in 3 iterations (with relative change=4.93543e-13)#>#> EM converged in 6 iterations (with relative change=2.39201e-15)#>#> EM converged in 117 iterations (with relative change=1.48713e-08)#>#> EM converged in 6 iterations (with relative change=1.00417e-13)#>#> Error in cut.default(x, q, labels = FALSE, include.lowest = TRUE): 'breaks' are not uniquefindClones(cna, by = 'arm')#> EM converged in 3 iterations (with relative change=1.13021e-09)#>#> EM converged in 7 iterations (with relative change=1.13481e-11)#>#> EM converged in 13 iterations (with relative change=9.20887e-13)#>#> EM converged in 15 iterations (with relative change=1.55184e-14)#>#> EM converged in 2 iterations (with relative change=4.02904e-11)#>#> EM converged in 7 iterations (with relative change=0)#>#> EM converged in 12 iterations (with relative change=6.10121e-15)#>#> EM converged in 19 iterations (with relative change=2.69694e-14)#>#> Error in cut.default(x, q, labels = FALSE, include.lowest = TRUE): 'breaks' are not unique