mergeVariantPosition: mergeVariantPosition

In mil2041/CNCDriver: CNCDriver

Description

mergeVariantPosition

Usage

mergeVariantPosition(datDF, sizeFactor, countsCutOff = 2)

Arguments

datDF	list of geneDF data frame
sizeFactor	sizeFactor vector, a parameter only used in pancancer calculation. A sizeFactor for total mutations counts normalization among multiple cancer types
countsCutOff	default is two, a parameter only used in pancancer calculation. Scale the mutation occurence value when the counts is equal or above countsCutOff

Value

collapsedDF 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.