Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes

chromosomeLength | Function to found max position for each chromosome |

consecutiveRuns | Function to detect consecutive runs in a vector (individual's... |

consecutiveRunsCpp | Function to detect consecutive runs in a vector (individual's... |

consecutiveRUNS.run | Main function to detect genomic RUNS (ROHom/ROHet) using the... |

createRUNdf | Function to create a dataframe of RUNS per individual animal... |

findOppositeAndMissing | Function to calculate oppositeAndMissingGenotypes array |

Froh_inbreeding | Function to calculated Froh genome-wide or chromosome-wide |

Froh_inbreedingClass | Function to calculated Froh using a ROH-class |

genoConvert | Convert 0/1/2 genotypes to 0/1 |

genoConvertCpp | Convert 0/1/2 genotypes to 0/1 |

heteroZygotTest | Function to check whether a window is (loosely) heterozygous... |

heteroZygotTestCpp | Function to check whether a window is (loosely) heterozygous... |

homoZygotTest | Function to check whether a window is (loosely) homozygous or... |

homoZygotTestCpp | Function to check whether a window is (loosely) homozygous or... |

pedConvertCpp | Convert ped genotypes to 0/1 |

plot_DistributionRuns | Plot Distribution of runs |

plot_InbreedingChr | Plot Froh-based inbreeding coefficients by group |

plot_manhattanRuns | Plot the proportion of times SNPs are inside runs - MANHATTAN... |

plot_PatternRuns | Plot sum of run-lengths (or average run-lengths) against the... |

plot_Runs | Function to plot runs per individual |

plot_SnpsInRuns | Plot the number of times each SNP falls inside runs |

plot_StackedRuns | Plot stacked runs |

plot_ViolinRuns | Violin plot of run length per individual (either sum or mean) |

readExternalRuns | Read runs from external files |

readPOPCpp | Function to return a dataframe of population (POP, ID) |

reorderDF | Function to reorder data frames by CHROMOSOME |

slidingRuns | Function to detect runs using sliding window approach |

slidingRUNS.run | Main function to detect RUNS (ROHom/ROHet) using sliding... |

slidingWindow | Function to slide a window over a vector (individual's... |

slidingWindowCpp | Function to slide a window over a vector (individual's... |

snpInRun | Function to return a vector of T/F for whether a SNP is or... |

snpInRunCpp | Function to return a vector of T/F for whether a SNP is or... |

snpInsideRuns | Function to count number of times a SNP is in a RUN |

snpInsideRunsCpp | Function to count number of times a SNP is in a RUN |

summaryRuns | Summary statistics on detected runs |

tableRuns | Function to retrieve most common runs in the population |

writeRUN | Function to write out RUNS per individual animal |

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