computeRandomizedResult: Randomly compute lists of driver mutations

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

Description

It renames the mutations in patMutMatrix with a randomized list of gene names and computes a list of driver mutations. It will repeat this process by numberOfRandomTests times. The result could be passed to the resultSummary method to calculate p-value for the driver mutations.

Usage

computeRandomizedResult(patMutMatrix, patOutMatrix, influenceGraph, 
geneNameList, outputFolder = NULL, printToConsole = FALSE, 
numberOfRandomTests = 500, weighted = FALSE, purturbGraph = FALSE, 
purturbData = TRUE)

Arguments

patMutMatrix	Patient Mutation Matrix
patOutMatrix	Patient Expression(Outlier) Matrix
influenceGraph	Influence Graph Matrix
geneNameList	A list of gene names that the new mutation names will be randomly chosen from.
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.
numberOfRandomTests	Number of lists of randomized driver mutations to be generated.
weighted	Must be set to FALSE in this version.
purturbGraph	Must be set to FALSE in this version.
purturbData	Must be set to TRUE in this version.

Value

A list of numeric vectors where each vector stores the number of events covered by the randomly identified drivers. The list can be passed to the resultSummary method to compute p-values.

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)
data(sampleGeneNames)

randomDriversResult = computeRandomizedResult(patMutMatrix=samplePatientMutationMatrix, 
patOutMatrix=samplePatientOutlierMatrix, influenceGraph=sampleInfluenceGraph, 
geneNameList=sampleGeneNames, outputFolder=NULL, printToConsole=FALSE, 
numberOfRandomTests=20, weight=FALSE, purturbGraph=FALSE, purturbData=TRUE)

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