coal {abctools}

Examples of coalescent data

Description

Data generated from a coalescent model for genetic variation.

Usage

data(coal)

Format

Matrices of parameters (first 2 columns) and summary statistics (remaining columns) from a coalescent model.

Details

"coal" contains 100,000 simulated datasets to use for an ABC analysis. "coalobs" contains 100 which can each be used as observed datasets. This allows methods to be tested on many different observations.

The parameters are the scaled mutation rate (theta) and scaled recombination rate (rho).

The summary statistics are the number of segregating sites (segsites), independent Uniform[0,25] random noise (unif), the pairwise mean number of nucleotidic differences (meandiff), the mean R^2 across pairs separated by < 10% of the simulated genomic regions (R2), the number of distinct haplotypes (nhap), the frequency of the most common haplotype (fhap), and the number of singleton haplotypes (shap).

To simulate a dataset 5,001 basepair DNA sequences for 50 individuals are generated from the coalescent model, with recombination, under the infinite-sites mutation model, using the software ms (Hudson 2002)

Data of this form has been analysed in several ABC papers. See the references for more details.

References

Blum, M. G. B., M. A. Nunes, D. Prangle and S. A. Sisson 'A comparative review of dimension reduction methods in approximate Bayesian computation' Statistical Applications in Genetics and Molecular Biology 13 (2014)

Hudson, R. R. 'Generating samples under a Wright-Fisher neutral model of genetic variation' Bioinformatics 18 (2002)

Joyce, P. and P. Marjoram 'Approximately sufficient statistics and Bayesian computation' Statistical Applications in Genetics and Molecular Biology 7 (2008)

Nunes, M. A. and D. J. Balding 'On optimal selection of summary statistics for approximate Bayesian computation' Statistical Applications in Genetics and Molecular Biology 9 (2010)

Nunes, M. A. and Prangle, D. abctools: an R package for tuning approximate Bayesian computation analyses. The R Journal 7 (2016)