as.adj.matrix: as.adj.matrix

In TRONCO: TRONCO, an R package for TRanslational ONCOlogy

Description

Extract the adjacency matrix of a TRONCO model. The matrix is indexed with colnames/rownames which represent genotype keys - these can be resolved with function keysToNames. It is possible to specify a subset of events to build the matrix, a subset of models if multiple reconstruction have been performed. Also, either the prima facie matrix or the post-regularization matrix can be extracted.

Usage

as.adj.matrix(x, events = as.events(x), models = names(x$model), type = "fit")

Arguments

x	A TRONCO model.
events	A subset of events as of as.events(x), all by default.
models	A subset of reconstructed models, all by default.
type	Either the prima facie ('pf') or the post-regularization ('fit') matrix, 'fit' by default.

Value

The adjacency matrix of a TRONCO model.

Examples

data(test_model)
as.adj.matrix(test_model)
as.adj.matrix(test_model, events=as.events(test_model)[5:15,])
as.adj.matrix(test_model, events=as.events(test_model)[5:15,], type='pf')

TRONCO documentation built on Nov. 8, 2020, 5:51 p.m.