CompositeDriver

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 (default value is 100000 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

Copyright © 2016-2017 Ekta Khurana Lab, WCMC

License

This project is licensed under the CC BY-NC 4.0