API for gerstung-lab/deepSNV
Detection of subclonal SNVs in deep sequencing data.
| Global functions | |
|---|---|
| .BSM | Source code |
| .MASequence | Source code |
| .deepSNV | Source code |
| .deepSNVsingle | Source code |
| .estimateDispersion | Source code |
| .makeVCFheader | Source code |
| .onLoad | Source code |
| .onUnload | Source code |
| .significantSNV | Source code |
| Extract | Man page |
| HIVmix | Man page |
| RCC | Man page |
| RF | Man page Source code |
| [,deepSNV,ANY,ANY,ANY-method | Man page |
| bam2R | Man page Source code |
| bbb | Man page Source code |
| betabinLRT | Man page |
| bf2Vcf | Man page Source code |
| consensusSequence | Man page |
| consensusSequence,deepSNV-method | Man page |
| consensusSequence,matrix-method | Man page |
| control | Man page |
| control,deepSNV-method | Man page |
| coordinates | Man page |
| coordinates,deepSNV-method | Man page |
| counts | Man page |
| dbetabinom | Man page Source code |
| deepSNV | Man page |
| deepSNV,character,character-method | Man page |
| deepSNV,character,matrix-method | Man page |
| deepSNV,deepSNV,missing-method | Man page |
| deepSNV,matrix,character-method | Man page |
| deepSNV,matrix,matrix-method | Man page |
| deepSNV-class | Man page |
| deepSNV-package | Man page |
| estimateDirichlet | Man page |
| estimateDirichlet,deepSNV-method | Man page |
| estimateDirichlet,matrix-method | Man page |
| estimateDispersion | Man page |
| estimateDispersion,deepSNV,missing-method | Man page |
| estimateDispersion,matrix,matrix-method | Man page |
| estimateRho | Man page Source code |
| loadAllData | Man page Source code |
| logbb | Source code |
| makePrior | Man page Source code |
| manhattanPlot | Man page Source code |
| mcChunk | Man page Source code |
| mutID | Source code |
| normalize | Man page |
| normalize,deepSNV,missing-method | Man page |
| normalize,matrix,matrix-method | Man page |
| p.combine | Man page Source code |
| p.val | Man page |
| p.val,deepSNV-method | Man page |
| pbetabinom | Man page Source code |
| phiX | Man page |
| pi | Man page |
| plot.deepSNV | Man page |
| qvals2Vcf | Man page Source code |
| regions2Coordinates | Source code |
| repeatMask | Man page |
| repeatMask,DNAString-method | Man page |
| repeatMask,deepSNV-method | Man page |
| select | Source code |
| shearwater | Man page |
| show,deepSNV-method | Man page |
| summary | Man page |
| summary,deepSNV-method | Man page |
| test | Man page |
| test,deepSNV-method | Man page |
| trueSNVs | Man page |
