DriverNet (version 1.12.0)

computeRandomizedResult: Randomly compute lists of driver mutations

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.

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)