CompositeDriver: An R repository from mil2041

CompositeDriver

Reference

Matthew H Bailey, Collin Tokheim, Eduard Porta Pardo, Sohini Sengupta, Denis Bertrand, Amila Weerasinghe, Antonio Colaprico, Michael C Wendl, Jaegil Kim, Brendan Reardon, Patrick Kwok Shing Ng, Kang Jin Jeong, Song Cao, Zixing Wang, Jianjiong Gao, Qingsong Gao, Fang Wang, Eric Minwei Liu, Loris Mularoni, Carlota Rubio Perez, Niranjan Nagarajan, Isidro Cortés Ciriano, Daniel Cui Zhou, Wen Wei Liang, Julian M Hess, Venkata D Yellapantula, David Tamborero, Abel Gonzalez Perez, Chayaporn Suphavilai, Jia Yu Ko, Ekta Khurana, Peter J Park, Eliezer M Van Allen, Han Liang, Michael S Lawrence, Adam Godzik, Nuria Lopez Bigas, Josh Stuart, David Wheeler, Gad Getz, Ken Chen, Alexander J Lazar, Gordon B Mills, Rachel Karchin, Li Ding, MC3 Working Group, Cancer Genome Atlas Research Network “Comprehensive Characterization of Cancer Driver Genes and Mutations”, Cell 173, 371 385.e18 (2018).

Overview

CompositeDriver combined mutation recurrence and functional impact to identify coding and non-coding cancer drivers

Version notes

CompositeDriver (version 0.2) supports SNV coding and non-coding drivers
CompositeDriver (version 0.1) supports SNV coding drivers

Installation

User will need to install devtools in R for running CompositeDriver package

install.packages("devtools")
library("devtools")
devtools::install_github("khuranalab/CompositeDriver")

Usage

User will need to

(1) download drm.gene.bed file and put it in the "/path/to/dataContext" folder
(2) assign "/path/to/Output.vcf" path for FunSeq2 annotated vcf file
(3) assign "/path/to/output" path for saving CompositeDriver results
(4) tumorType: name of tumor type
(5) seedNum: random number seed number (default is 42)
(6) functionalImpactScoreCDS: name of functional impact scoring scheme for CDS (current supports "FunSeq2" or "MCAP")
(7) functionalImpactScoreNonCoding: name of functional impact scoring scheme for non-coding (current supports "FunSeq2" )
(8) reSampleIter: sampling iterations (suggesting number is 1000000 iterations)
(9) useCores: number of cores for parellel computation

library(CompositeDriver)

#####
# global parameters setup
#####

  dataContextDir<-"/path/to/dataContext"
  annotatedInput<-"/path/to/Output.vcf"
  outputDir<-"/path/to/output"
  tumorType<-"GBM"
  seedNum<-42
  functionalImpactScoreCDS<-"FunSeq2"
  functionalImpactScoreNonCoding<-"FunSeq2"
  reSampleIter<-1000
  useCores<-6
  debugMode<-FALSE

#####
  
  preProcessVCF(annotatedInput,functionalImpactScoreCDS,functionalImpactScoreNonCoding,outputDir,tumorType,useCores)

#####

  mutationType<-"CDS"
  cdsOutputDf<-getCDSpvalue(outputDir,tumorType,mutationType,
                            reSampleIter=reSampleIter,
                            seedNum=seedNum,debugMode=debugMode)

#####

Contacts

For any questions, comments and suggestions, please email

ekk2003 [at] med.cornell.edu
mil2041 [at] med.cornell.edu

License

This project is licensed under the CC BY-NC 4.0

mil2041/CompositeDriver