Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

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Documentation for package ‘MMAPPR2’ version 1.18.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

MMAPPR2-package	Mutation Mapping Analysis Pipeline for Pooled RNA-seq
calculateDistance	Read BAM files and generate Euclidean distance data
candidates	MmapprData Getters
candidates-method	MmapprData Getters
distance	MmapprData Getters
distance-method	MmapprData Getters
distancePower	MmapprParam Getters and Setters
distancePower-method	MmapprParam Getters and Setters
distancePower<-	MmapprParam Getters and Setters
distancePower<--method	MmapprParam Getters and Setters
fileAggregation	MmapprParam Getters and Setters
fileAggregation-method	MmapprParam Getters and Setters
fileAggregation<-	MmapprParam Getters and Setters
fileAggregation<--method	MmapprParam Getters and Setters
generateCandidates	Generate potential causative mutations and consequences in peak regions
homozygoteCutoff	MmapprParam Getters and Setters
homozygoteCutoff-method	MmapprParam Getters and Setters
homozygoteCutoff<-	MmapprParam Getters and Setters
homozygoteCutoff<--method	MmapprParam Getters and Setters
loessFit	Perform optimized Loess regression for each chromosome
loessOptCutFactor	MmapprParam Getters and Setters
loessOptCutFactor-method	MmapprParam Getters and Setters
loessOptCutFactor<-	MmapprParam Getters and Setters
loessOptCutFactor<--method	MmapprParam Getters and Setters
loessOptResolution	MmapprParam Getters and Setters
loessOptResolution-method	MmapprParam Getters and Setters
loessOptResolution<-	MmapprParam Getters and Setters
loessOptResolution<--method	MmapprParam Getters and Setters
minBaseQuality	MmapprParam Getters and Setters
minBaseQuality-method	MmapprParam Getters and Setters
minBaseQuality<-	MmapprParam Getters and Setters
minBaseQuality<--method	MmapprParam Getters and Setters
minDepth	MmapprParam Getters and Setters
minDepth-method	MmapprParam Getters and Setters
minDepth<-	MmapprParam Getters and Setters
minDepth<--method	MmapprParam Getters and Setters
minMapQuality	MmapprParam Getters and Setters
minMapQuality-method	MmapprParam Getters and Setters
minMapQuality<-	MmapprParam Getters and Setters
minMapQuality<--method	MmapprParam Getters and Setters
mmappr	Mutation Mapping Analysis Pipeline for Pooled RNA-Seq
MMAPPR2	Mutation Mapping Analysis Pipeline for Pooled RNA-seq
MmapprData	MmapprData Class
MmapprData-class	MmapprData Class
MmapprData-getters	MmapprData Getters
MmapprParam	MmapprParam Class and Constructor
MmapprParam-class	MmapprParam Class and Constructor
MmapprParam-functions	MmapprParam Getters and Setters
mutFiles	MmapprParam Getters and Setters
mutFiles-method	MmapprParam Getters and Setters
mutFiles<-	MmapprParam Getters and Setters
mutFiles<--method	MmapprParam Getters and Setters
naCutoff	MmapprParam Getters and Setters
naCutoff-method	MmapprParam Getters and Setters
naCutoff<-	MmapprParam Getters and Setters
naCutoff<--method	MmapprParam Getters and Setters
outputFolder	MmapprParam Getters and Setters
outputFolder-method	MmapprParam Getters and Setters
outputFolder<-	MmapprParam Getters and Setters
outputFolder<--method	MmapprParam Getters and Setters
outputMmapprData	Generate plots and tables from MMAPPR2 data
param	MmapprData Getters
param-method	MmapprData Getters
peakIntervalWidth	MmapprParam Getters and Setters
peakIntervalWidth-method	MmapprParam Getters and Setters
peakIntervalWidth<-	MmapprParam Getters and Setters
peakIntervalWidth<--method	MmapprParam Getters and Setters
peakRefinement	Characterize Euclidean distance peaks using resampling simulation
peaks	MmapprData Getters
peaks-method	MmapprData Getters
prePeak	Identify chromosomes containing peaks
refFasta	MmapprParam Getters and Setters
refFasta-method	MmapprParam Getters and Setters
refFasta<-	MmapprParam Getters and Setters
refFasta<--method	MmapprParam Getters and Setters
refGenome	MmapprParam Getters and Setters
refGenome-method	MmapprParam Getters and Setters
refGenome<-	MmapprParam Getters and Setters
refGenome<--method	MmapprParam Getters and Setters
species	MmapprParam Getters and Setters
species-method	MmapprParam Getters and Setters
species<-	MmapprParam Getters and Setters
species<--method	MmapprParam Getters and Setters
tempOutputFolder	Generate temporary output folder
vepFlags	MmapprParam Getters and Setters
vepFlags-method	MmapprParam Getters and Setters
vepFlags<-	MmapprParam Getters and Setters
vepFlags<--method	MmapprParam Getters and Setters
wtFiles	MmapprParam Getters and Setters
wtFiles-method	MmapprParam Getters and Setters
wtFiles<-	MmapprParam Getters and Setters
wtFiles<--method	MmapprParam Getters and Setters