Fst {snpStats} | R Documentation

## 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

    Fst(snps, group, pairwise=FALSE)

### Arguments

`snps` | an object of class `SnpMatrix` or `XSnpMatrix` containing the SNP data
`group` | a factor (or object than can be coerced into a factor), of length equal to the number of rows of `snps`, giving the grouping or rows for which the Fst is to be calculated
`pairwise` | if `TRUE`, the within-group variances are weighted according to the number of possible within-group pairwise comparisons of chromosomes. If `FALSE`, the default value, weights are simply the number of chromosomes in each group.

### 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

    ## Analysis of some HapMap data

    data(for.exercise)
    f <- Fst(snps.10, subject.support$stratum)
    weighted.mean(f$Fst, f$weight)

[Package snpStats version 1.40.0 Index]