# calculate.pairwise.Fst: Calculates unbiased pairwise Fst between a pair of... 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 a pair of populations/individuals. Loci for which either of the populations/individuals has missing data (i.e. - the sample size is zero) are excluded.

## Usage

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

## Arguments

 `allele.counts` A matrix of allele counts of dimensions `nrow = ` 2, one for each of the two populations/individuals between which pairwise F_{ST} is being calculated, and `ncol = ` the number of loci genotyped. `sample.sizes` A matrix of sample sizes of dimensions `nrow = ` 2, one for each of the two populations/individuals between which pairwise F_{ST} is being calculated, and `ncol = ` the number of loci genotyped (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

Pairwise unbiased F_{ST} between a pair of populations/individuals

Gideon Bradburd

## 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``` ```#With the HGDP dataset data(HGDP.bedassle.data) #Draw 2 populations at random from the Eurasian HGDP dataset pop1 <- sample(nrow(HGDP.bedassle.data\$allele.counts),1) pop2 <- sample(nrow(HGDP.bedassle.data\$allele.counts),1) #Calculate unbiased Fst between them pairwise.Fst <- calculate.pairwise.Fst( HGDP.bedassle.data\$allele.counts[c(pop1,pop2),], HGDP.bedassle.data\$sample.sizes[c(pop1,pop2),] ) #Print that Fst to the console print(sprintf("Fst between the %s population and the %s population is %s", HGDP.bedassle.data\$hgdp.metadata[pop1,1], HGDP.bedassle.data\$hgdp.metadata[pop2,1], round(pairwise.Fst,3)) ) ```

### Example output

``` "Fst between the Mongola population and the French population is 0.094"
```

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