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

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DriverNet is a package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph, which is a gene-gene interaction network deduced from pathway data. A greedy algorithm is used to find the possible driver genes, which may mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.

Author
Ali Bashashati, Reza Haffari, Jiarui Ding, Gavin Ha, Kenneth Liu, Jamie Rosner and Sohrab Shah
Date of publication
None
Maintainer
Jiarui Ding <jiaruid@cs.ubc.ca>
License
GPL-3
Version
1.14.0

View on Bioconductor

Man pages

actualEvents
Actual events covered by driver mutations
computeDrivers
Compute a list of driver mutations
computeRandomizedResult
Randomly compute lists of driver mutations
DriverNet-package
Drivernet: uncovering somatic driver mutations modulating...
DriverNetResult-class
Class '"DriverNetResult"'
drivers
List of driver mutations identified by DriverNet
getPatientOutlierMatrix
Compute the patient outlier matrix
preprocessMatrices
Remove unnecessary entries from matrices
resultSummary
Summarize result for drivers ranking.
sampleDriversList
Sample DriverNet result
sampleGeneNames
Sample gene names
sampleInfluenceGraph
Sample influence graph
samplePatientExpressionMatrix
Sample patient expression matrix
samplePatientMutationMatrix
Sample patient mutation matrix
samplePatientOutlierMatrix
Sample patient outlier matrix
sampleRandomDriversResult
Sample Result from computeRandomizedResult
totalEvents
Total number of events in the data

Files in this package

DriverNet/DESCRIPTION
DriverNet/NAMESPACE
DriverNet/R
DriverNet/R/AllClasses.R
DriverNet/R/AllGenerics.R
DriverNet/R/ComputeDrivers.R
DriverNet/R/DriverSelection.R
DriverNet/R/Graph.R
DriverNet/R/Preprocessing.R
DriverNet/R/ResultSummary.R
DriverNet/R/SignificanceTest.R
DriverNet/R/getPatientOutlierMatrix.R
DriverNet/R/methods-DriverNetResult.R
DriverNet/build
DriverNet/build/vignette.rds
DriverNet/data
DriverNet/data/datalist
DriverNet/data/sampleDriversList.rda
DriverNet/data/sampleGeneNames.rda
DriverNet/data/sampleInfluenceGraph.rda
DriverNet/data/samplePatientExpressionMatrix.rda
DriverNet/data/samplePatientMutationMatrix.rda
DriverNet/data/samplePatientOutlierMatrix.rda
DriverNet/data/sampleRandomDriversResult.rda
DriverNet/inst
DriverNet/inst/doc
DriverNet/inst/doc/DriverNet-Overview.R
DriverNet/inst/doc/DriverNet-Overview.Rnw
DriverNet/inst/doc/DriverNet-Overview.pdf
DriverNet/man
DriverNet/man/DriverNet-package.Rd
DriverNet/man/DriverNetResult-class.Rd
DriverNet/man/actualEvents.Rd
DriverNet/man/computeDrivers.Rd
DriverNet/man/computeRandomizedResult.Rd
DriverNet/man/drivers.Rd
DriverNet/man/getPatientOutlierMatrix.Rd
DriverNet/man/preprocessMatrices.Rd
DriverNet/man/resultSummary.Rd
DriverNet/man/sampleDriversList.Rd
DriverNet/man/sampleGeneNames.Rd
DriverNet/man/sampleInfluenceGraph.Rd
DriverNet/man/samplePatientExpressionMatrix.Rd
DriverNet/man/samplePatientMutationMatrix.Rd
DriverNet/man/samplePatientOutlierMatrix.Rd
DriverNet/man/sampleRandomDriversResult.Rd
DriverNet/man/totalEvents.Rd
DriverNet/vignettes
DriverNet/vignettes/DriverNet-Overview.Rnw
DriverNet/vignettes/drivernet.bib