Evaluation of Genotyping Error in Genotype-by-Sequencing Data

bin_depths | bin read depths of SNPs into categories having at least S... |

estimate_m_rd | Estimate heterozygote miscall rate for different read depth... |

exp_and_obs_geno_freqs | Computed expected and observed genotype frequencies from a... |

geno_freq_boundaries | function to return a tibble with the min/max values of... |

geno_freq_calc_single | from on 012 file compute expected (assuming HW equilbrium)... |

geno_freqs_scatter | return a 'ggplot2' plot object of observed and expected... |

gibbsM | simulate a new miscall rate for each read depth category... |

gibbsP | simulate new reference allele frequencies from their beta... |

gibbsX | compute full conditional for each X given Y, p, R, and m, and... |

infer_m | get posterior estimates for m from different read depth... |

lobster_buz_2000 | Restriction-associated digest (RAD) sequence data from 36... |

lobster_buz_2000_as_012_matrix | An 012 matrix from (RAD) sequence data from 36 lobsters at... |

make_it_012 | just a quick function for making an 012 matrix from a... |

posteriors_plot | return a 'ggplot2' plot object of the posterior esimates for... |

prep_vcf_for_est_m_rd | convert a VCF into an 012,-1 matrix and read_depth bin matrix... |

tidy_m_ests | tidy up the estimate_m_rd output into something you can plot |

whoa | whoa: Evaluation of genotyping error in genotype by... |

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