Bayesian approach for detecting copy number alterations from single cell RNA-seq data

calcAlleleCnvProb | Run BADGER allele-only model to assess posterior probability... |

calcCombCnvProb | Run BADGER combined model to assess posterior probability of... |

calcErrorRate | Calculate effective error rate |

calcGexpCnvProb | Run BADGER expression-only model to assess posterior... |

clafProfile | Composite Minor Allele Frequency (CLAF) Profile plot |

geneFactors | Returns a factor vector across pos (chr:pos vector)... |

getAlleleCount | Get alternative allele count for positions of interest |

getCoverage | Get coverage count for positions of interest |

insideCnvs | Returns a vector of T/F depending on whether SNPs are in CNV... |

mvFit | Estimate expression magnitude variance as a function of... |

normalizedExpression | Normalize gene expression to a normal reference for... |

plotExpHeatmap | Visualize expression heatmap by chromosome for... |

pointsWithin | Determine if a point is within a range |

pos2GRanges | From data frame of positions to GRanges object |

range2GRanges | From data frame of ranges to GRanges object |

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