Phase template strands from Strand-seq data

assembleHaps | This will take sorted matrices and will calculate concordance... |

bamregion2GRanges | Import BAM file into GRanges |

calcMatrixScore | This function calculates score of a matrix as a sum of... |

compareSingleCellHaps | This will take sorted matrices and will calculate concordance... |

exportBedGraph | Generates a bedgraph from GRanges object in order to upload... |

exportConsensus | This funcion will load sorted watson and crick matrices and... |

exportVCF | Generates a VCF file from phased haplotypes |

fillGapsWithBam | This function will take both assembled haplotypes and will... |

fillGapsWithVCF | This function will take both assembled haplotypes and will... |

loadGRangesFromFiles | Load phased data from RData files |

loadMatrices | This funcion will read in partial single cell haplotypes into... |

LOHseeker | This function uses circular-binary-segementation to segment... |

phaseChromosome | Wrapper function for StrandPhaseR |

plotHapDensity | This function will take phased data for each chromosome and... |

plotPhasedReads | This function will take phased reads for each chromosome and... |

plotSingleCellHaps | This function will take phased data for each chromosome and... |

readConfig | Read StrandPhaseR configuration file |

sortMatrices | This funcion will load initial watson and crick matrices and... |

splitReads | This will take phased info for each haplotype and will split... |

strandPhaseR | Wrapper function |

vcf2ranges | Read VCF file into a 'GRanges' object |

writeConfig | Write StrandPhaseR configuration file |

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