as.pathway: as.pathway

In TRONCO: TRONCO, an R package for TRanslational ONCOlogy

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')

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