getLincRNAPvalue: Run CNCDriver lincRNA p-value calculation

Description Usage Arguments Value Examples

View source: R/getLincRNAPvalue.R

Description

Run CNCDriver lincRNA p-value calculation

Usage

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getLincRNAPvalue(
  inputFileDir,
  outputFileDir,
  lincRNARegionBedFile,
  elementKeyWord = "lincRNA",
  triNucleotideDistributionFile,
  filterOutBlacklistMutations,
  mutationBlacklistFile,
  replicationTimingGenomeBinnedFile,
  replicationTimingElementBinnedFile,
  tumorType,
  mutationType,
  cellType,
  replicationTimingCutOff,
  seedNum = 42,
  reSampleIterations,
  reRunPvalueCutOff = 0.1,
  useCores,
  taskNum,
  unitSize,
  debugMode = FALSE
)

Arguments

inputFileDir

The path for prepared R object file [for example,reducedFunseqOutputNCDS_GBM.Rd]

outputFileDir

The path for output files

lincRNARegionBedFile

The defintion of promoter regions in bed file format

elementKeyWord

Default is "lincRNA", the keyword of lincRNA annotation in FunSeq2

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

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#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.