as.pathway {TRONCO} | R Documentation

## as.pathway

### Description

Given a cohort and a pathway, return the cohort with events restricted to genes involved in the pathway. This might contain a new 'pathway' genotype with an alteration mark if any of the involved genes are altered.

### Usage

    as.pathway(
      x,
      pathway.genes,
      pathway.name,
      pathway.color = "yellow",
      aggregate.pathway = TRUE,
      silent = FALSE
    )

### Arguments

`x` | A TRONCO compliant dataset.
`pathway.genes` | Gene (symbols) involved in the pathway.
`pathway.name` | Pathway name for visualization.
`pathway.color` | Pathway color for visualization.
`aggregate.pathway` | If TRUE drop the events for the genes in the pathway.
`silent` | A parameter to disable/enable verbose messages.

### Value

Extract the subset of events for genes which are part of a pathway.

### Examples

    data(test_dataset)
    p = as.pathway(test_dataset, c('ASXL1', 'TET2'), 'test_pathway')

[Package TRONCO version 2.20.1 Index]