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

## Calculates unbiased pairwise Fst between a pair of populations

### Description

This function calculates unbiased `F_{ST}`

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

, 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

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

### Arguments

`allele.counts` |
A matrix of allele counts of dimensions |

`sample.sizes` |
A matrix of sample sizes of dimensions |

### Value

Pairwise unbiased `F_{ST}`

between a pair of populations/individuals

### 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)
#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))
)
```

*BEDASSLE*version 1.6.1 Index]