get_features: Return summary features for the cohort.

In caravagn/revolver: REVOLVER - Repeated Evolution in Cancer

Return summary features for the cohort.

Description

Computes a set of summary features for the cohort, in the form of a matrix. The fits must be available inside the cohort to retrieve some of these features, which are:

• the matrix of driver events with mean CCF or binary value;

• the matrix of the drivers occurrence acrross all the cohort;

• the matrix of the clonal drivers occurrence acrross all the cohort;

• the matrix of the subclonal drivers occurrence acrross all the cohort;

• the matrix of the occurrence of all evolutionary trajectories across patients

The function returns a named list, so that names can be used to access the matrices.

Usage

get_features(x, patients = x$patients)

Arguments

x	A REVOLVER cohort.
patients	A vector of patient ids for which the features are extracted.

Value

A list of matrices.

See Also

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

Examples

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

features = get_features(TRACERx_NEJM_2017_REVOLVER)

print(names(features))

print(features)

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