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], "_datasets": [ { "name": "dgrp2.3R.5k.data", "title": "A subset of sequencing data from the Drosophila Genetics Reference Panel", "object": "dgrp2.3R.5k.data", "file": "dgrp2.3R.5k.data.rda", "class": [ "genomeadmixr_data" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "GenomeAdmixR-package", "title": "Simulate Admixture of Genomes", "topics": [ "GenomeAdmixR-package", "GenomeAdmixR" ] }, { "page": "ancestry_module", "title": "Creates a module to start simulations tracking local ancestry", "topics": [ "ancestry_module" ] }, { "page": "calculate_allele_frequencies", "title": "Calculate allele frequencies", "topics": [ "calculate_allele_frequencies" ] }, { "page": "calculate_average_ld", "title": "Calculates the ld between two alleles", "topics": [ "calculate_average_ld" ] }, { "page": "calculate_dist_junctions", "title": "collect the full distribution of junctions in the population", "topics": [ "calculate_dist_junctions" ] }, { "page": "calculate_fst", "title": "Calculate FST", "topics": [ "calculate_fst" ] }, { "page": "calculate_heterozygosity", "title": "Calculate heterozygosity", "topics": [ "calculate_heterozygosity" ] }, { "page": "calculate_ld", "title": "Calculate linkage disequilibrium statistics This function calculates two matrices, once containing all pairwise linkage disequilibrium (ld) values, and one matrix containing all pairwise r statistics", "topics": [ "calculate_ld" ] }, { "page": "calculate_marker_frequency", "title": "Calculate allele frequencies at a specific marker location", "topics": [ "calculate_marker_frequency" ] }, { "page": "combine_input_data", "title": "combine sequence data that was previously read from file into a population", "topics": [ "combine_input_data" ] }, { "page": "create_artificial_genomeadmixr_data", "title": "function to generate artificial genomeadmixr_data", "topics": [ "create_artificial_genomeadmixr_data" ] }, { "page": "create_iso_female", "title": "function to simulate creation of an isofemale line", "topics": [ "create_iso_female" ] }, { "page": "dgrp2.3R.5k.data", "title": "A subset of sequencing data from the Drosophila Genetics Reference Panel", "topics": [ "dgrp2.3R.5k.data" ] }, { "page": "iso_female_ancestry", "title": "Create isofemale", "topics": [ "iso_female_ancestry" ] }, { "page": "iso_female_sequence", "title": "Create isofemale", "topics": [ "iso_female_sequence" ] }, { "page": "load_population", "title": "Load a population from file", "topics": [ "load_population" ] }, { "page": "migration_settings", "title": "Function to manage settings associated with migration", "topics": [ "migration_settings" ] }, { "page": "plink_to_genomeadmixr_data", "title": "function to convert plink style (ped/map) data to genome_admixr_data", "topics": [ "plink_to_genomeadmixr_data" ] }, { "page": "plot_chromosome", "title": "plots a chromosome", "topics": [ "plot_chromosome" ] }, { "page": "plot_difference_frequencies", "title": "Plot the change in frequency between the start and end of a simulation", "topics": [ "plot_difference_frequencies" ] }, { "page": "plot_dist_junctions", "title": "plot the distribution of junctions", "topics": [ "plot_dist_junctions" ] }, { "page": "plot_frequencies", "title": "Plot the frequencies of all ancestors along the genome.", "topics": [ "plot_frequencies" ] }, { "page": "plot_joyplot_frequencies", "title": "make a joy plot of the distribution of allele frequencies within a region", "topics": [ "plot_joyplot_frequencies" ] }, { "page": "plot_over_time", "title": "Plot the frequencies of all ancestors over time", "topics": [ "plot_over_time" ] }, { "page": "plot_start_end", "title": "Plot both the starting frequencies and the final frequencies in one plot", "topics": [ "plot_start_end" ] }, { "page": "plot.individual", "title": "plot the genome of an individual", "topics": [ "plot.individual" ] }, { "page": "print.genomeadmixr_data", "title": "print an individual to the console", "topics": [ "print.genomeadmixr_data" ] }, { "page": "print.individual", "title": "print an individual to the console", "topics": [ "print.individual" ] }, { "page": "print.population", "title": "print a population object", "topics": [ "print.population" ] }, { "page": "read_input_data", "title": "read sequence data from file to be used in simulation", "topics": [ "read_input_data" ] }, { "page": "save_population", "title": "Save a population to file", "topics": [ "save_population" ] }, { "page": "sequence_module", "title": "create sequence module", "topics": [ "sequence_module" ] }, { "page": "simulate_admixture", "title": "Individual based simulation of the breakdown of contiguous ancestry blocks.", "topics": [ "simulate_admixture" ] }, { "page": "simulate_ancestry", "title": "Individual based simulation of the breakdown of contiguous ancestry blocks.", "topics": [ "simulate_ancestry" ] }, { "page": "simulate_ancestry_migration", "title": "Individual based simulation of the breakdown of 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