Description Usage Arguments Details Value Author(s)

`checkSNP`

helps to filter for those SNPs that are best suited for estimating Ne.

1 |

`p0` |
numeric vector of relative starting allele frequencies ( |

`pt` |
numeric vector of relative allele frequencies after |

`cov0` |
numeric vector of sequencing coverage at the first time point. |

`covt` |
numeric vector of sequencing coverage at the second time point. |

`truncAF` |
numeric indicating whether SNPs with extreme allele frequencies should be excluded for Ne estimation. If |

Alleles that start from a frequency of `0`

or `1`

are not informative for Ne estimation and `checkSNP`

will return `FALSE`

for those ones. Similarly positions with a sequencing coverage of 0 will be masked, and `checkSNP`

will return `FALSE`

.

Extreme allele frequencies, which are close to `0`

or `1`

, increase the variance of Ne estimates and it might therefore be advantageous not to consider them for Ne estimation. The parameter `truncAF`

can be used for this purpose.

A logical vector indicating which SNPs are suited for Ne estimation.

Thomas Taus

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