Detection of subclonal SNVs in deep sequencing data.

bam2R | Read nucleotide counts from a .bam file |

betabinLRT | ShearwaterML |

bf2Vcf | Function to create a 'VCF' object with variant calls from an... |

consensusSequence-methods | Calculate the consensus sequence. |

control-methods | Get control counts |

coordinates-methods | Get coordinates |

counts | Example count table |

dbetabinom | Beta-binomial probability distribution |

deepSNV-class | deepSNV class. |

deepSNV-methods | Test two matched deep sequencing experiments for... |

deepSNV-package | Detection of subclonal SNVs in deep sequencing experiments |

estimateDirichlet-methods | Learn a base-specific Dirichlet prior. |

estimateDispersion-methods | Estimate the Dispersion factor in a beta-binomial model. |

estimateRho | Helper function for estimating the dispersion factor rho |

Extract-methods | Subsetting for deepSNV objects. |

loadAllData | Function to load all data from a list of bam files |

makePrior | Compute a prior from a COSMIC VCF object |

manhattanPlot | Manhattan plot. |

mcChunk | Little helper function to split the count objects into a... |

normalize-methods | Normalize nucleotide counts. |

pbetabinom | Cumulative beta-binomial probability distribution |

p.combine | Combine two p-values |

phiX | Example phiX data |

pi | Example prior |

plot.deepSNV | Scatter plot of relative nucleotide frequencies. |

p.val-methods | Get p-values |

qvals2Vcf | Function to create a 'VCF' object with variant calls from an... |

RCC | Example RCC data |

repeatMask-methods | Mask homopolymeric repeats. |

RF | Relative frequencies. |

shearwater | Bayesian beta-binomal test, codename shearwater |

show-deepSNV-method | Show method for deepSNV objects |

summary-methods | Summary of a deepSNV object |

test-methods | Get test counts |

trueSNVs | Example .bam data and true SNVs. |

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