ITransfer: Extract the information transfer available for a patient.

In caravagn/revolver: REVOLVER - Repeated Evolution in Cancer

Extract the information transfer 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). Besides, it can return the information transfer as the ordering of the annotated drivers, or in terms o the ordering of the clones these map to.

Usage

ITransfer(x, p, rank = 1, type = "drivers", data = "trees")

Arguments

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

Value

The information transfer for the tree of a patient

See Also

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

Examples

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

# Get the transfer among drivers, top-ranking tree
ITransfer(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002', rank = 1, type = 'drivers')

# Get the transfer among clones, top-ranking tree
ITransfer(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002', rank = 1, type = 'clones')

# Get the transfer from the fit
ITransfer(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002', rank = 1, type = 'clones', data = 'fits')
ITransfer(TRACERx_NEJM_2017_REVOLVER, 'CRUK0002', rank = 1, type = 'drivers', data = 'fits')

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