snpStats: Fst – R documentation

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Fst

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)

snpStats

SnpMatrix and XSnpMatrix classes and methods

v1.40.0

GPL-3

Authors

David Clayton <dc208@cam.ac.uk>

Initial release

2019-10-08

Fst