# Calculate fixation indices

### Description

This function calculates the fixation index Fst for each SNP, together with its weight in the overall estimate (as used by the Internation HapMap Consortium).

### Usage

1 |

### Arguments

`snps` |
an object of class |

`group` |
a factor (or object than can be coerced into a factor),
of length equal to the number of rows of |

`pairwise` |
if |

### Details

See vignette.

### Value

A list:

- Fst
Fst values for each SNP

- weight
The weights for combining these into a single index

### Note

Uncertain genotypes are treated as missing

### Author(s)

David Clayton dc208@cam.ac.uk

### Examples

1 2 3 4 5 | ```
## Analysis of some HapMap data
data(for.exercise)
f <- Fst(snps.10, subject.support$stratum)
weighted.mean(f$Fst, f$weight)
``` |