View source: R/facets-emcncf2.R
emcncf2 | R Documentation |
Uses genotype mixture model to estimate copy number, cellular fraction, and subclonal structures. \ Uses estimates based on the cnlr.median and mafR as initial values for the EM iteration.
emcncf2( x, trace = FALSE, unif = FALSE, min.nhet = 15, maxiter = 10, difcf = 0.05, maxk = 5, eps = 0.001 )
x |
(list) the output from procSample. This function uses the elements jointseg, out and dipLogR from the output. |
trace |
(logical) flag to print the EM criteria at every step |
unif |
(logical) random EM start values of cellular fractions instead of clusteredcncf values |
min.nhet |
(numeric) minimum number of heterozygote snps in a segment used to call minor cn |
maxiter |
(numeric) maximum number of EM iterations |
difcf |
(numeric) the minimal difference between segment cluster specific cellular fraction estimate and clonally constrained estimate for declaring candidate subclonal events |
maxk |
(numeric) maximum number of clonal and subclonal clusters allowed for the fit |
eps |
(numeric) the convergence threshold |
A list containing:
loglik |
loglikelihood value of the fitted model |
purity |
fraction tumor cells in the tumor sample |
ploidy |
average total copy number of the tumor cells |
dipLogR |
estimated logR value of diploid segments |
cncf |
dataframe consisting of the columns of segmentation output as well as cellular fraction (cf), total (tcn) and lesser (lcn) copy number of each segment and their em counterpart (with .em suffix), and a clonal.cluster indicater with clonal.cluster=1 indicating the clonal cluster and a higher number (2,3, etc..) indicating subclonal clusters. |
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