Phylo: Extract the trees available for a patient.

In caravagn/revolver: REVOLVER - Repeated Evolution in Cancer

Extract the trees available for a patient.

Description

From a cohort object, this function extracts the tree objects that are available for a patient. Parameters can be set to retrieve a particular tree, or the fit tree which is however availble only after fitting the cohort data. This function can either return a phylogenetic clone tree (R object ctree), or mutation trees (R object btree).

Usage

Phylo(x, p, rank = NULL, data = "trees")

Arguments

x	A REVOLVER cohort.
p	The id of a patient in the cohort.
rank	The rank of the tree to extract.
data	Either 'trees' or 'fit', which requires to have already computed the fit of the input cohort.

Value

Phylogenetic or mutation trees data for the patient.

See Also

Other Getters: CCF_clusters(), CCF(), Clonal_cluster(), Data(), Drivers(), ITransfer(), Samples(), Subclonal(), Truncal(), get_features()

Examples

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

# Get all the trees for a patient
Phylo(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002')

# Get a specific tree for a patient
Phylo(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002', rank = 2)
# Get the fit tree for a patient

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