Get a clonal tree from a configuration matrix
variant x clone matrix of binary values. The clone-variant configuration, which encodes the phylogenetic tree structure. This is the output Z of Canopy
a one-column numeric matrix encoding the (observed or estimated) prevalence (or frequency) of each clone
character(1), a character string defining the strictness of
the function if there are all-zero rows in the Config matrix. If
Output tree may be nonsensical if the input
Config matrix does not
define a coherent tree structure.
An object of class "phylo" describing the tree structure. The output object
also contains an element "sna" defining the clustering of variants onto the
branches of the tree, and if
P is non-null it also contains VAF
(variant allele frequency), CCF (cell clone fraction) and clone prevalence
values (computed from the supplied
1 2 3
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