API for MMAPPR2
Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

Global functions
.aiccOpt Source code
.avgFiles Source code
.calcDistForChr Source code
.checkDep Source code
.customPrint Source code
.defaultOutputFolder Source code
.densityScoreAndOrderVariants Source code
.filterVariants Source code
.getFileReadChrList Source code
.getLoess Source code
.getPeakFromTopP Source code
.getPeakRange Source code
.getSubsampleLoessMax Source code
.getVariantsForRange Source code
.homozygoteFilter Source code
.indexBamFileList Source code
.localMin Source code
.localResolution Source code
.loessFitForChr Source code
.log Source code
.medianForChr Source code
.messageAndLog Source code
.minTwo Source code
.naFilter Source code
.numDecimals Source code
.peakRefinementChr Source code
.plotGenomeDistance Source code
.plotPeaks Source code
.prepareOutputFolder Source code
.runVEPForVariants Source code
.samtoolsPileup Source code
.stDevForChr Source code
.tmpPeakVcf Source code
.validBamFiles Source code
.validFastaFile Source code
.validMmapprParam Source code
.validVepFlags Source code
.writeCandidateTables Source code
MMAPPR2 Man page
MMAPPR2-package Man page
MmapprData Man page
MmapprData-class Man page
MmapprData-getters Man page
MmapprParam Man page Source code
MmapprParam-class Man page
MmapprParam-functions Man page
calculateDistance Man page Source code
candidates Man page
candidates,MmapprData-method Man page
distance Man page
distance,MmapprData-method Man page
distancePower Man page
distancePower,MmapprParam-method Man page
distancePower<- Man page
distancePower<-,MmapprParam-method Man page
fileAggregation Man page
fileAggregation,MmapprParam-method Man page
fileAggregation<- Man page
fileAggregation<-,MmapprParam-method Man page
generateCandidates Man page Source code
homozygoteCutoff Man page
homozygoteCutoff,MmapprParam-method Man page
homozygoteCutoff<- Man page
homozygoteCutoff<-,MmapprParam-method Man page
loessFit Man page Source code
loessOptCutFactor Man page
loessOptCutFactor,MmapprParam-method Man page
loessOptCutFactor<- Man page
loessOptCutFactor<-,MmapprParam-method Man page
loessOptResolution Man page
loessOptResolution,MmapprParam-method Man page
loessOptResolution<- Man page
loessOptResolution<-,MmapprParam-method Man page
minBaseQuality Man page
minBaseQuality,MmapprParam-method Man page
minBaseQuality<- Man page
minBaseQuality<-,MmapprParam-method Man page
minDepth Man page
minDepth,MmapprParam-method Man page
minDepth<- Man page
minDepth<-,MmapprParam-method Man page
minMapQuality Man page
minMapQuality,MmapprParam-method Man page
minMapQuality<- Man page
minMapQuality<-,MmapprParam-method Man page
mmappr Man page Source code
mutFiles Man page
mutFiles,MmapprParam-method Man page
mutFiles<- Man page
mutFiles<-,MmapprParam-method Man page
naCutoff Man page
naCutoff,MmapprParam-method Man page
naCutoff<- Man page
naCutoff<-,MmapprParam-method Man page
outputFolder Man page
outputFolder,MmapprParam-method Man page
outputFolder<- Man page
outputFolder<-,MmapprParam-method Man page
outputMmapprData Man page Source code
param Man page
param,MmapprData-method Man page
peakIntervalWidth Man page
peakIntervalWidth,MmapprParam-method Man page
peakIntervalWidth<- Man page
peakIntervalWidth<-,MmapprParam-method Man page
peakRefinement Man page Source code
peaks Man page
peaks,MmapprData-method Man page
prePeak Man page Source code
refFasta Man page
refFasta,MmapprParam-method Man page
refFasta<- Man page
refFasta<-,MmapprParam-method Man page
refGenome Man page
refGenome,MmapprParam-method Man page
refGenome<- Man page
refGenome<-,MmapprParam-method Man page
species Man page
species,MmapprParam-method Man page
species<- Man page
species<-,MmapprParam-method Man page
tempOutputFolder Man page Source code
vepFlags Man page
vepFlags,MmapprParam-method Man page
vepFlags<- Man page
vepFlags<-,MmapprParam-method Man page
wtFiles Man page
wtFiles,MmapprParam-method Man page
wtFiles<- Man page
wtFiles<-,MmapprParam-method Man page
MMAPPR2 documentation built on April 29, 2020, 3:30 a.m.