computeRandomizedResult {DriverNet} | R Documentation |
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.
computeRandomizedResult(patMutMatrix, patOutMatrix, influenceGraph, geneNameList, outputFolder = NULL, printToConsole = FALSE, numberOfRandomTests = 500, weighted = FALSE, purturbGraph = FALSE, purturbData = TRUE)
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. |
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.
Ali Bashashati, Reza Haffari, Jiarui Ding, Gavin Ha, Kenneth Liu, Jamie Rosner and Sohrab Shah
Maintainer: Jiarui Ding <jiaruid@cs.ubc.ca>
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)