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 |