Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/allele.sharing.R

Internal function of Demerelate to calculate different allele sharing indices or estimators for any pair of population.

1 2 3 | ```
allele.sharing(pop1, pop2, allele.column, data,
value = NA, ref.pop)
``` |

`pop1` |
Specific dataframe of type inputformat. Population one used for calculations. Inputformat needs to be standard three digits mode for Demerelate. |

`pop2` |
Specific dataframe of type inputformat. Population two used for calculations. Inputformat needs to be standard three digits mode for Demerelate. |

`allele.column` |
Numeric value - It equals the number of the first column in the dataframe containing allele information. Order of loci in both populations needs to be exactly equal. |

`data` |
If set as TRUE allele sharing is only calculated for each pairwise comparison of individuals in the same position in pop1 with this position in pop2 - i.e. the diagonal of a distance matrix. If set as data.frame each pairwise comparison of column 1 with column 2 is calculated - i.e. the lower triangle of a distance matrix. |

`value` |
Character defining method to calculate allele sharing or similarity estimates. Can be set as "Bxy", "Sxy", "Mxy", "Li", "rxy", "lxy", "loiselle", "wang.fin", "wang", "ritland", "morans.fin" or "morans". |

`ref.pop` |
Reference population used for relatedness calculations. |

The function uses each population to build a dataframe with row positions for pairwise comparisons according to their position in `pop1`

and `pop2`

. Similarity indices are calculated for each pair in one locus defined by the number indicated in `allele.column`

. If `allele.column`

is set as `1`

allele information will be taken from the two columns of the first locus.

Function returns the object simil.vector as vector of similarities according to `value`

.

Philipp Kraemer, <[email protected]>

```
inputformat
Demerelate
Emp.calc
Bxy
Sxy
Mxy
Li
rxy
lxy
loiselle
wang.fin
wang
ritland
morans.fin
```

1 2 3 | ```
## internal function not intended for direct use
``` |

Demerelate documentation built on May 30, 2017, 8:14 a.m.

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