![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| 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 |