Compute binary mutation trees for a patient (phylogenies).

Create mutation tree phylogenies from the package mtree, fitting the input data given to REVOLVER. A set of patient ids can be given as input, by default all are used. A parameter controls if you want to overwrite the trees of the patient, where they already computed. Please refer to the parameters of the mtree constructor from package mtree for the input parameters that you can use to tune the construction.

compute_mutation_trees(
  x,
  patients = Stats_cohort(x) %>% pull(patientID),
  overwrite = FALSE,
  ...
)

Arguments

x

A REVOLVER cohort.

patients

A set of patient ids in the cohort, for which the phylogenies are created.

overwrite

If TRUE, recompute trees even if already available.

...

Additional parameters forwarded to the mtree constructor.

Value

A REVOLVER cohort with mutation tree phylogenies for the requested patients.

See also

Other Cohort creation: CCF_parser(), compute_clone_trees(), input_custom_trees(), revolver_check_cohort(), revolver_cohort()

Examples

if (FALSE) { # \dontrun{
data('TRACERx_NEJM_2017_REVOLVER', package = 'evoverse.datasets')
x = compute_mutation_trees(TRACERx_NEJM_2017_REVOLVER)
} # }