Tools for building migratory bird genoscapes

compile_assayable | return SNPs and say whether the are assayable or not, along... |

comp_pair | make a comparison between two groups that are in df |

convert_012_to_bed | create a PLINK bed file from and 012 matrix |

correct_ass_prob | from vectors of snp allele freqs, compute the expected prob... |

geno_freq_calcs | from on 012 file compute expected and observed genotype... |

geno_freq_calc_single | from on 012 file compute expected and observed genotype... |

genoscape_pca | do a PCA using SNPRelate and prepare output for rapid... |

genoscapeRtools | My package documentation <e2><80><a6> bla bla <e2><80><a6> |

ggplot_the_Qs | ggplot the Qs from multiple runs of ADMIXTURE |

group_012_cnts | count up number of observed alleles in each group |

hohz_windows_1 | compute fraction of heterozygous and homozygous and missing... |

hwe_exact_test | perform exact tests of H-W disequilibrium for each locus... |

mat_cumul_cpp | return a matrix of cumumlative sums along the rows or colums |

miss_curves_indv | Order a genotype matrix by individual missingness at... |

miss_curves_locus | Order a genotype matrix by locus missingness at different... |

pairwise_fst | compute pairwise Fst using SNPRelate |

pipe | Pipe operator |

qprob_rando_raster | return an RGB raster of colors to depict breeding pops on a... |

read_012 | read a set of 012 files from vcftools into a matrix of... |

read_angsd_geno_probs | read an angsd binary genotype probability file |

run_admixture | run admixture Reps times at each of K values |

sample_from_angsd_probs | Sample a genotype (0,1,2) from probabilities for all the snps... |

scan_012 | read a set of 012 files from vcftools into a matrix of... |

slurp_admixture | read in all the AMIXTURE files that are in the r_X_K_Y... |

testHWE | a quick function to do the HW exact test on on an open gds... |

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