computeRandomizedResult {DriverNet} | R Documentation

## 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.

### Author(s)

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

Maintainer: Jiarui Ding <jiaruid@cs.ubc.ca>

### 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)

[Package DriverNet version 1.28.0 Index]