calculate.all.pairwise.Fst {BEDASSLE} | R Documentation |

## Calculates unbiased pairwise Fst between all sampled populations

### Description

This function calculates unbiased `F_{ST}`

(based on Weir and Hill's `\theta`

,
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

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

### Arguments

`allele.counts` |
A matrix of allelic count data, for which |

`sample.sizes` |
A matrix of sample sizes, for which |

### Value

A matrix of pairwise, unbiased `F_{ST}`

.

### Author(s)

Gideon Bradburd

### References

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

### Examples

```
#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"))
```

*BEDASSLE*version 1.6.1 Index]