as.adj.matrix {TRONCO} | R Documentation

## as.adj.matrix

### 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')

[Package TRONCO version 2.12.0 Index]