View source: R/sumstat_omega.R

sumstat_omega | R Documentation |

Calculates the Omega Statistic introduced by Kim & Nielsen (2004) from the simulated data. The statistic is sensitive for hard selective sweeps. To calculate the statistic, coala relies on the command line program OmegaPlus, which needs to be downloaded and compiled manually in order to use the statistic.

```
sumstat_omega(
name = "omega",
min_win = 100,
max_win = 1000,
grid = 1000,
binary = "automatic",
transformation = identity
)
```

`name` |
The name of the summary statistic. When simulating a model, the value of the statistics are written to an entry of the returned list with this name. Summary statistic names must be unique in a model. |

`min_win` |
The minimum distance from the grid point that a SNP must have to be included in the calculation of omega. |

`max_win` |
The maximum distance from the grid point that a SNP must have to be included in the calculation of omega. |

`grid` |
The number of points for which omega is calculated on each locus. Should be significantly lower than the locus length. |

`binary` |
The path of the binary for OmegaPlus. If set to "automatic", coala will try to find a binary called "OmegaPlus" using the PATH environment variable. |

`transformation` |
An optional function for transforming the results of the statistic. If specified, the results of the transformation are returned instead of the original values. |

A data frame listing of locus, genetic position and the calculated omega value.

Linkage disequilibrium as a signature of selective sweeps. Y. Kim and R. Nielsen (2004). Genetics, 167, 1513-1524.

OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets. N. Alachiotis, A. Stamatakis and P. Pavlidis (2012). Bioinformatics Vol. 28 no. 17 2012, pages 2274-2275 doi:10.1093/bioinformatics/bts419

To create a demographic model: `coal_model`

To calculate this statistic from data: `calc_sumstats_from_data`

Other summary statistics:
`sumstat_dna()`

,
`sumstat_file()`

,
`sumstat_four_gamete()`

,
`sumstat_ihh()`

,
`sumstat_jsfs()`

,
`sumstat_mcmf()`

,
`sumstat_nucleotide_div()`

,
`sumstat_seg_sites()`

,
`sumstat_sfs()`

,
`sumstat_tajimas_d()`

,
`sumstat_trees()`

```
## Not run:
model <- coal_model(20, 1, 50000) +
feat_recombination(50) +
feat_mutation(1000) +
feat_selection(strength_A = 1000, time = 0.03) +
sumstat_omega()
stats <- simulate(model)
plot(stats$omega$omega, type = "l")
## End(Not run)
```

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