Calculate fixation indices

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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

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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

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## Analysis of some HapMap data

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

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