mutate_microsats: A function to mutate microsatellites
In andersgs/microsimr: Simulate microsatellite data using Hudson's ms program

Description Usage Arguments Details References

A function to mutate microsatellites

1 2	mutate_microsats(n_mutations, mutation_model = "smm", p_single = 0.8, sigma2 = 50)

`n_mutations`	A vector indicating the total number of mutations along each branch of a tree
`mutation_model`	A character string indicating the mutation model to use. Currently, only the strict stepwise mutation model of Ohta and Kimura (1973) ('smm'), and the DiRienzo et al. (1994) two-phase model ('tpm') are implemented. Default is 'smm'
`p_single`	Probability of a single-step mutation to be used in the 'tmp' model
`sigma2`	Variance in allele size to be used in the 'tpm' model

A tree is first simulated using 'ms'. Mutations are simulated along the branches of the tree following a Poisson distribution with lambda proportional to branch length times theta (4Nmu). This first part is done in sim_microsats.

Here, the number of mutations at each branch is transformed to either a loss or gain in number of repeats. In the 'smm' model, each mutation represents either a loss or gain of a single repeat unit with equal probability. In the 'tpm' model, with probability p_single a mutation represents either a gain or loss of a single repeat, and with probability (1 - p_single) the gain/loss is larger following a symmetric geometric distribution.

Please refer to the vignette to see a deeper explanation, and test of each model.

Di Rienzo, A., Peterson, A. C., Garza, J. C., Valdes, A. M., Slatkin, M., & Freimer, N. B. (1994). Mutational processes of simple-sequence repeat loci in human populations. Proceedings of the National Academy of Sciences of the United States of America, 91(8), 3166–3170.

Ohta, T., & Kimura, M. (2007). A model of mutation appropriate to estimate the number of electrophoretically detectable alleles in a finite population. Genetical Research, 89(5-6), 367–370. http://doi.org/10.1017/S0016672308009531

andersgs/microsimr documentation built on May 12, 2019, 2:42 a.m.