getCDSPvalueWithPreFilter2: Run CNCDriver coding region (CDS) p-value calculation with...

In mil2041/CNCDriver: CNCDriver

Description

Run CNCDriver coding region (CDS) p-value calculation with mutation pre-filtering

Usage

getCDSPvalueWithPreFilter2(
  inputFileDir,
  outputFileDir,
  codingRegionBedFile,
  elementKeyWord = "CDS",
  proteinDomainFile,
  proteinLengthFile,
  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
)

Arguments

inputFileDir	The path for prepared R object file [for example,reducedFunseqOutputCDS_GBM.Rd]
outputFileDir	The path for output files
codingRegionBedFile	The defintion of coding regions in bed file format
elementKeyWord	Default is "Promoter", the keyword of promoter annotation in FunSeq2
proteinDomainFile	protein domain information from pfam
proteinLengthFile	protein length information from ensembl
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

Value

results data frame

Examples

#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)

mil2041/CNCDriver documentation built on Dec. 13, 2020, 3:41 a.m.