Simulate Admixture of Genomes

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Documentation for package ‘GenomeAdmixR’ version 2.1.12

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

GenomeAdmixR-package	Simulate Admixture of Genomes
ancestry_module	Creates a module to start simulations tracking local ancestry
calculate_allele_frequencies	Calculate allele frequencies
calculate_average_ld	Calculates the ld between two alleles
calculate_dist_junctions	collect the full distribution of junctions in the population
calculate_fst	Calculate FST
calculate_heterozygosity	Calculate heterozygosity
calculate_ld	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
calculate_marker_frequency	Calculate allele frequencies at a specific marker location
combine_input_data	combine sequence data that was previously read from file into a population
create_artificial_genomeadmixr_data	function to generate artificial genomeadmixr_data
create_iso_female	function to simulate creation of an isofemale line
dgrp2.3R.5k.data	A subset of sequencing data from the Drosophila Genetics Reference Panel
GenomeAdmixR	Simulate Admixture of Genomes
iso_female_ancestry	Create isofemale
iso_female_sequence	Create isofemale
load_population	Load a population from file
migration_settings	Function to manage settings associated with migration
plink_to_genomeadmixr_data	function to convert plink style (ped/map) data to genome_admixr_data
plot.individual	plot the genome of an individual
plot_chromosome	plots a chromosome
plot_difference_frequencies	Plot the change in frequency between the start and end of a simulation
plot_dist_junctions	plot the distribution of junctions
plot_frequencies	Plot the frequencies of all ancestors along the genome.
plot_joyplot_frequencies	make a joy plot of the distribution of allele frequencies within a region
plot_over_time	Plot the frequencies of all ancestors over time
plot_start_end	Plot both the starting frequencies and the final frequencies in one plot
print.genomeadmixr_data	print an individual to the console
print.individual	print an individual to the console
print.population	print a population object
read_input_data	read sequence data from file to be used in simulation
save_population	Save a population to file
sequence_module	create sequence module
simulate_admixture	Individual based simulation of the breakdown of contiguous ancestry blocks.
simulate_ancestry	Individual based simulation of the breakdown of contiguous ancestry blocks.
simulate_ancestry_migration	Individual based simulation of the breakdown of contiguous ancestry blocks in two populations linked by migration
simulate_sequence	Individual based simulation of the breakdown of contiguous ancestry blocks.
simulate_sequence_migration	Individual based simulation of the breakdown of contiguous ancestry blocks in two populations linked by migration
simulation_data_to_genomeadmixr_data	function to convert ped/map data to genome_admixr_data
vcfR_to_genomeadmixr_data	function to convert a vcfR object to genome_admixr_data
write_as_plink	function to write simulation output as PLINK style data