calculatePvalueWithMutCategoryDistributionMatched7: calculate Pvalue With Mut CategoryDistribution Matched

In mil2041/CNCDriver: CNCDriver

Description

calculate Pvalue With Mut CategoryDistribution Matched

Usage

calculatePvalueWithMutCategoryDistributionMatched7(
  variantTriMutCategory,
  backgroundPosVariant,
  mutationDistMatrix,
  featureDF,
  reSampleNum,
  replaceFlag = FALSE,
  replicationTimingCutOff,
  debugFileName,
  debugMode = FALSE
)

Arguments

variantTriMutCategory	variantTriMutCategory data frame
backgroundPosVariant	backgroundPosVariant data frame
mutationDistMatrix	mutationDistMatrix data frame
featureDF	featureDF data frame
reSampleNum	number of re-sampling iterations
replaceFlag	default is FALSE, whether to replace or not in the sampling process
replicationTimingCutOff,	Default is 0.2, a numeric value ranging from 0 to 1
debugFileName	fileName to output debug information
debugMode	default is FALSE, TRUE or FALSE

Value

variantTriMutCategoryParsed 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.