| Title: | Simulating the Evolution of Biological Sequences |
|---|---|
| Description: | A coalescent simulator that allows the rapid simulation of biological sequences under neutral models of evolution, see Staab et al. (2015) <doi:10.1093/bioinformatics/btu861>. Different to other coalescent based simulations, it has an optional approximation parameter that allows for high accuracy while maintaining a linear run time cost for long sequences. It is optimized for simulating massive data sets as produced by Next- Generation Sequencing technologies for up to several thousand sequences. |
| Authors: | Paul Staab [aut, cph], Zhu Sha [aut, cph], Dirk Metzler [aut, cre, cph, ths], Gerton Lunter [aut, cph, ths] |
| Maintainer: | Dirk Metzler <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 1.7.5 |
| Built: | 2024-11-12 05:57:43 UTC |
| Source: | https://github.com/scrm/scrm-r |
The Sequential Coalescent with Recombination Model (SCRM) is an approximation of the Ancestral Recombination Graph. It can be used to simulate the neutral evolution of chromosomes/biological sequences subject to possibly complicated population structure. The program scrm is an implementation of this model that is designed to act as an drop-in replacement for the widely adopted coalescent simulator ms. This package contains scrm along with an R interface.
Paul Staab, Zhu Sha, Dirk Metzler & Gerton Lunter
Maintainer: Paul Staab [email protected]
scrm for details on how to use scrm,
vignette('scrm-Arguments') for an overview of command line arguments and
vignette('scrm-TreesForApe') for an example on using
genealogies simulated with scrm with package 'ape'.
This function provides an interface for calling scrm from R.
The command line options are passed via the args argument.
The vignette 'scrm-Arguments' contains details about the available options.
Summary statistics are converted into an R format. Additionally, there
is an option to write the original command line output into a file.
scrm(args, file = "")scrm(args, file = "")
args |
A string containing the command-line arguments for scrm. Look at scrms vignette for a description of available arguments. |
file |
If provided, scrm will additionally write it is output into a file with the given file, using an ms-like text output. |
A named list of summary statistics. Most summary statistics are again a list, where each entry contains the value for one locus. For the site frequency spectrum, the summary statistic is a matrix, where each row contains the spectrum for one locus.
The R version of scrm uses random number from R's random generator.
Therefore, the '-seed' argument of the command-line version will be ignored,
and no seed is given in the output.
Use the R function set.seed prior to calling this
function to ensure reproducibility of results.
vignette('scrm-Arguments') for an overview of command line arguments and
vignette('scrm-TreesForApe') for an example on using
genealogies simulated with scrm with package 'ape'.
set.seed(789) # 5 Chromosomes with 100 bases each with recombination and mutation sum_stats <- scrm('5 1 -r 3.1 100 -t 1.5 -T -L') str(sum_stats) # Simulate the site frequency spectrum at 3 loci. For each locus # 10 Chromosomes of 1Mb length are sampled from two populations with # migration inbetween. scrm('10 3 -r 400 1000000 -l 100000 -I 2 4 6 0.5 -t 300 -oSFS')$sfsset.seed(789) # 5 Chromosomes with 100 bases each with recombination and mutation sum_stats <- scrm('5 1 -r 3.1 100 -t 1.5 -T -L') str(sum_stats) # Simulate the site frequency spectrum at 3 loci. For each locus # 10 Chromosomes of 1Mb length are sampled from two populations with # migration inbetween. scrm('10 3 -r 400 1000000 -l 100000 -I 2 4 6 0.5 -t 300 -oSFS')$sfs