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