Man pages for GenomeAdmixR
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... |
| calculate_marker_frequency | Calculate allele frequencies at a specific marker location |
| combine_input_data | combine sequence data that was previously read from file into... |
| create_artificial_genomeadmixr_data | function to generate artificial genomeadmixr_data |
| create_iso_female | function to simulate creation of an isofemale line |
| default_params_doc | Default parameter documentation |
| dgrp2.3R.5k.data | A subset of sequencing data from the Drosophila Genetics... |
| GenomeAdmixR-package | 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... |
| plot_chromosome | plots a chromosome |
| plot_difference_frequencies | Plot the change in frequency between the start and end of a... |
| plot_dist_junctions | plot the distribution of junctions |
| plot_frequencies | Plot the frequencies of all ancestors along the genome. |
| plot.individual | plot the genome of an individual |
| plot_joyplot_frequencies | make a joy plot of the distribution of allele frequencies... |
| plot_over_time | Plot the frequencies of all ancestors over time |
| plot_start_end | Plot both the starting frequencies and the final frequencies... |
| 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... |
| simulate_ancestry | Individual based simulation of the breakdown of contiguous... |
| simulate_ancestry_migration | Individual based simulation of the breakdown of contiguous... |
| simulate_sequence | Individual based simulation of the breakdown of contiguous... |
| simulate_sequence_migration | Individual based simulation of the breakdown of contiguous... |
| 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 |
