get5utrPvalueWithPreFilter: Run CNCDriver 5'UTR p-value calculation with mutation...
In mil2041/CNCDriver: CNCDriver

Description Usage Arguments Value Examples

Run CNCDriver 5'UTR p-value calculation with mutation pre-filtering

get5utrPvalueWithPreFilter(
  inputFileDir,
  outputFileDir,
  promoterRegionBedFile,
  elementKeyWord = "UTR",
  minPoints = 2,
  dRadius = 50,
  triNucleotideDistributionFile,
  filterOutBlacklistMutations,
  mutationBlacklistFile,
  replicationTimingGenomeBinnedFile,
  replicationTimingElementBinnedFile,
  tumorType,
  mutationType,
  cellType,
  replicationTimingCutOff,
  seedNum = 42,
  reSampleIterations,
  reRunPvalueCutOff = 0.1,
  useCores = 1,
  taskNum = 0,
  unitSize,
  debugMode = FALSE
)

`inputFileDir`	The path for prepared R object file [for example,reducedFunseqOutputNCDS_GBM.Rd]
`outputFileDir`	The path for output files
`promoterRegionBedFile`	The defintion of promoter regions in bed file format
`elementKeyWord`	Default is "Promoter", the keyword of promoter annotation in FunSeq2
`minPoints`	default is 2 [ unit: samples ]
`dRadius`	default is 50 [ unit: bp ]
`triNucleotideDistributionFile`	Cancer type specific mutation counts in 96 trinucleotide category
`filterOutBlacklistMutations`	TRUE or FALSE
`mutationBlacklistFile`	The file for mutation blacklist regions
`replicationTimingGenomeBinnedFile`	Replication timing value at 1MB bin
`replicationTimingElementBinnedFile`	Replication timing value of each element within 1MB bin
`tumorType`	Study name
`mutationType`	User provided mutated gene list
`cellType`	Cell type of the study, [ BJ, GM12878, HeLaS3, HepG2, IMR90, K562, MCF7, SKNSH or average ]
`replicationTimingCutOff`	Default is 0.2, a numeric value ranging from 0 to 1
`seedNum`	User provided random number seed, default is 42
`reSampleIterations`	User provided re-sapling iteration numbers
`reRunPvalueCutOff`	Default is 0.1, a numeric value ranging from 0 to 1
`useCores`	Default is 1, number of cpu to use
`taskNum`	Default is 0, 0 means to run all elements
`unitSize`	Number of elements to run per task
`debugMode`	TRUE or FALSE

results data frame

#date<-getRunDates(latest=TRUE)
cancerType<-"KIRC"
selectedSampleId<-NA
#worDir<-getwd()
mutSig2CVthreshold<-0.1
rareMutationUpperLimit<-0.3
rareMutationLowerLimit<-0.1
rareMutationFreq<-0.02

#runNetBox2(dataDir,cancerType,
#           mutationList,ampGeneList,delGeneList,epiSilencedList,
#           mutationFreq,ampGeneFreq,delGeneFreq,epiSilencedFreq,
#           pathwayCommonsDb,directed,
#           linkerPValThreshold,communityDetectionMethod,
#           keepIsolatedNodes,verbose=TRUE)