computeDrivers: Compute a list of driver mutations

In DriverNet: Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer

Description

Use a greedy algorithm to rank a list of driver mutations.

Usage

computeDrivers(patMutMatrix, patOutMatrix, influenceGraph, outputFolder = NULL, 
printToConsole = FALSE, weighted = FALSE)

Arguments

patMutMatrix	Patient Mutation Matrix
patOutMatrix	Patient Outlier Matrix
influenceGraph	Influence Graph Matrix
outputFolder	The folder to store the log. If set to NULL, no log files will be written. If set to "", the log will be written to the current folder.
printToConsole	If set to TRUE, progress and result of the function will be printed to the console.
weighted	Must be set to FALSE in this version.

Value

An object of DriverNetResult class that can be passed to the resultSummary method.

Author(s)

Ali Bashashati, Reza Haffari, Jiarui Ding, Gavin Ha, Kenneth Liu, Jamie Rosner and Sohrab Shah

Maintainer: Jiarui Ding <[e-mail]>

Examples

data(samplePatientMutationMatrix)
data(samplePatientOutlierMatrix)
data(sampleInfluenceGraph)
driversList = computeDrivers(samplePatientMutationMatrix, samplePatientOutlierMatrix, 
sampleInfluenceGraph, outputFolder=NULL, printToConsole=FALSE)

drivers(driversList)[1:10]

DriverNet documentation built on Nov. 8, 2020, 10:59 p.m.