extractElementMutations: Extract overlapping mutations from element annotation bed...

In mil2041/CNCDriver: CNCDriver

Description

Extract overlapping mutations from element annotation bed file

Usage

extractElementMutations(elementBedfile, reducedFunseqOutput, debugMode = FALSE)

Arguments

elementBedfile	The data frame for element annotated bed file
reducedFunseqOutput	reducedFunseq2 data frame
debugMode	TRUE or FALSE

Value

reducedFunseq2 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.