Package: GenomeAdmixR 2.1.8

GenomeAdmixR: Simulate Admixture of Genomes

Individual-based simulations forward in time, simulating how patterns in ancestry along the genome change after admixture. Full description can be found in Janzen (2021) <doi:10.1111/2041-210X.13612>.

Authors:Thijs Janzen [aut, cre], Fernando Diaz G. [ctb], Richèl J.C. Bilderbeek [ctb]

GenomeAdmixR_2.1.8.tar.gz
GenomeAdmixR_2.1.8.zip(r-4.5)GenomeAdmixR_2.1.8.zip(r-4.4)GenomeAdmixR_2.1.8.zip(r-4.3)
GenomeAdmixR_2.1.8.tgz(r-4.4-arm64)
GenomeAdmixR_2.1.8.tar.gz(r-4.5-noble)GenomeAdmixR_2.1.8.tar.gz(r-4.4-noble)
GenomeAdmixR.pdf |GenomeAdmixR.html✨
GenomeAdmixR/json (API)

# Install 'GenomeAdmixR' in R:
install.packages('GenomeAdmixR', repos = c('https://thijsjanzen.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/thijsjanzen/genomeadmixr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • dgrp2.3R.5k.data - A subset of sequencing data from the Drosophila Genetics Reference Panel

On CRAN:

5.24 score 5 stars 14 scripts 247 downloads 32 exports 81 dependencies

Last updated 9 months agofrom:e4269d1f1a. Checks:OK: 1 ERROR: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-win-x86_64ERROROct 11 2024
R-4.5-linux-x86_64ERROROct 12 2024
R-4.4-win-x86_64ERROROct 12 2024
R-4.3-win-x86_64ERRORSep 10 2024

Exports:ancestry_modulecalculate_allele_frequenciescalculate_average_ldcalculate_dist_junctionscalculate_fstcalculate_heterozygositycalculate_ldcalculate_marker_frequencycombine_input_datacreate_artificial_genomeadmixr_datacreate_iso_femaleiso_female_ancestryiso_female_sequenceload_populationmigration_settingsplink_to_genomeadmixr_dataplot_chromosomeplot_difference_frequenciesplot_dist_junctionsplot_frequenciesplot_joyplot_frequenciesplot_over_timeplot_start_endread_input_datasave_populationsequence_modulesimulate_admixturesimulate_ancestry_migrationsimulate_sequence_migrationsimulation_data_to_genomeadmixr_datavcfR_to_genomeadmixr_datawrite_as_plink

Dependencies:ade4adegenetapebase64encbootbslibcachemcliclustercolorspacecommonmarkcpp11crayondigestdplyrfansifarverfastmapfontawesomefsgastongenericsggplot2ggridgesgluegtablegtoolshierfstathtmltoolshttpuvigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisememusemgcvmimemunsellnlmepermutepillarpinfsc50pixmappkgconfigplyrpromisesR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelreshape2rlangsassscalessegmentedseqinrshinysourcetoolsspstringistringrtibbletidyselectutf8vcfRvctrsveganviridisLitewithrxtable

Demonstrate isofemales

Rendered fromDemonstrate_isofemales.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2021-02-25
Started: 2018-11-21

Demonstrate joyplot

Rendered fromJoyplots.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2021-02-24
Started: 2018-11-21

Empirical data

Rendered fromEmpirical_data.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2021-02-25
Started: 2021-01-28

Visualization

Thijs Janzen

Rendered fromVisualization.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2021-02-24
Started: 2021-01-13

Walkthrough

Rendered fromWalkthrough.Rmdusingknitr::rmarkdownon Oct 10 2024.

Last update: 2021-02-25
Started: 2018-11-21

Readme and manuals

Help Manual

Help pageTopics
Simulate Admixture of GenomesGenomeAdmixR-package GenomeAdmixR
Creates a module to start simulations tracking local ancestryancestry_module
Calculate allele frequenciescalculate_allele_frequencies
Calculates the ld between two allelescalculate_average_ld
collect the full distribution of junctions in the populationcalculate_dist_junctions
Calculate FSTcalculate_fst
Calculate heterozygositycalculate_heterozygosity
Calculate linkage disequilibrium statistics This function calculates two matrices, once containing all pairwise linkage disequilibrium (ld) values, and one matrix containing all pairwise r statisticscalculate_ld
Calculate allele frequencies at a specific marker locationcalculate_marker_frequency
combine sequence data that was previously read from file into a populationcombine_input_data
function to generate artificial genomeadmixr_datacreate_artificial_genomeadmixr_data
function to simulate creation of an isofemale linecreate_iso_female
A subset of sequencing data from the Drosophila Genetics Reference Paneldgrp2.3R.5k.data
Create isofemaleiso_female_ancestry
Create isofemaleiso_female_sequence
Load a population from fileload_population
Function to manage settings associated with migrationmigration_settings
function to convert plink style (ped/map) data to genome_admixr_dataplink_to_genomeadmixr_data
plots a chromosomeplot_chromosome
Plot the change in frequency between the start and end of a simulationplot_difference_frequencies
plot the distribution of junctionsplot_dist_junctions
Plot the frequencies of all ancestors along the genome.plot_frequencies
make a joy plot of the distribution of allele frequencies within a regionplot_joyplot_frequencies
Plot the frequencies of all ancestors over timeplot_over_time
Plot both the starting frequencies and the final frequencies in one plotplot_start_end
plot the genome of an individualplot.individual
print an individual to the consoleprint.genomeadmixr_data
print an individual to the consoleprint.individual
print a population objectprint.population
read sequence data from file to be used in simulationread_input_data
Save a population to filesave_population
create sequence modulesequence_module
Individual based simulation of the breakdown of contiguous ancestry blocks.simulate_admixture
Individual based simulation of the breakdown of contiguous ancestry blocks.simulate_ancestry
Individual based simulation of the breakdown of contiguous ancestry blocks in two populations linked by migrationsimulate_ancestry_migration
Individual based simulation of the breakdown of contiguous ancestry blocks.simulate_sequence
Individual based simulation of the breakdown of contiguous ancestry blocks in two populations linked by migrationsimulate_sequence_migration
function to convert ped/map data to genome_admixr_datasimulation_data_to_genomeadmixr_data
function to convert a vcfR object to genome_admixr_datavcfR_to_genomeadmixr_data
function to write simulation output as PLINK style datawrite_as_plink