# calculate.all.pairwise.Fst: Calculates unbiased pairwise Fst between all sampled... In BEDASSLE: Quantifies effects of geo/eco distance on genetic differentiation

## Description

This function calculates unbiased F_{ST} (based on Weir and Hill's θ, 2002), between all populations/individuals included in the `counts` matrix, and returns the results in a `k` by `k` matrix, where `k = nrow(counts)`. Loci for which either of the populations/individuals has missing data (i.e. - the sample size is zero) are excluded.

## Usage

 `1` ```calculate.all.pairwise.Fst(allele.counts, sample.sizes) ```

## Arguments

 `allele.counts` A matrix of allelic count data, for which `nrow = ` the number of populations and `ncol = ` the number of bi-allelic loci sampled. Each cell gives the number of times allele ‘1’ is observed in each population. The choice of which allele is allele ‘1’ is arbitrary, but must be consistent across all populations at a locus. `sample.sizes` A matrix of sample sizes, for which `nrow = ` the number of populations and `ncol = ` the number of bi-allelic loci sampled (i.e. - the dimensions of `sample.sizes` must match those of `counts`). Each cell gives the number of chromosomes successfully genotyped at each locus in each population.

## Value

A matrix of pairwise, unbiased F_{ST}.

## References

Weir,B.S. and W.G. Hill. 2002. Estimating F-statistics. Ann.Rev.Gen. 36:949-952.

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20``` ```#With the HGDP dataset data(HGDP.bedassle.data) #Calculate pairwise Fst between all population pairs hgdp.pairwise.Fst <- calculate.all.pairwise.Fst( HGDP.bedassle.data\$allele.counts, HGDP.bedassle.data\$sample.sizes ) #Plot pairwise Fst against geographic distance plot(HGDP.bedassle.data\$GeoDistance, hgdp.pairwise.Fst, pch=19, col=HGDP.bedassle.data\$EcoDistance+1, ylab="pairwise Fst", xlab="geographic distance", main="isolation by distance") legend(x="bottomright",pch=19,col=c(1,2), legend=c("same side of Himalayas", "opposite sides of Himalayas")) ```

### Example output

```
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BEDASSLE documentation built on May 2, 2019, 6:10 a.m.