compute_clone_trees: Compute CCF-based clone trees for a patient (phylogenies).

In caravagn/revolver: REVOLVER - Repeated Evolution in Cancer

Compute CCF-based clone trees for a patient (phylogenies).

Description

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

Usage

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

Arguments

x	A REVOLVER cohort with now available phylogeneis for the required patients.
patients	A set of patient ids in the cohort, for which the phylogenies are created.

See Also

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

Examples

# Data released in the 'evoverse.datasets'
data('TRACERx_NEJM_2017_REVOLVER', package = 'evoverse.datasets')

print(TRACERx_NEJM_2017_REVOLVER)

# We use the standard parameters with overwrite = TRUE
# otherwise the computation skips the patient
TRACERx_NEJM_2017_REVOLVER = compute_clone_trees(
   TRACERx_NEJM_2017_REVOLVER,
   patients = "CRUK0002",
   overwrite = TRUE)

Phylo(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002', rank = 1)

caravagn/revolver documentation built on May 21, 2022, 5:48 p.m.