weir.fst.plink: Compute Weir & Cockerham's F_st estimator using PLINK

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Compute Weir & Cockerham's F_st estimator using PLINK

Usage

weir.fst.plink(prefix, by = NULL, per.locus = FALSE, chr = NULL,
  flags = "", ...)

Arguments

prefix	a pointer to a PLINK fileset (of class plink)
by	a vector of population labels; if not specified, family ID is used
per.locus	logical: if TRUE, return one value per marker; else return aggregate
chr	restrict analysis to this chromosome (if NULL, all chromosomes)
flags	command-line flags passed directly to underlying PLINK call
...	ignored

Details

The F_st statistic as proposed by Sewall Wright is a measure of allele-frequency differentiation between two populations. See the relevant PLINK documentation for details of the underlying calculations, and Weir & Cockerham (1984) for derivation of the estimator.

Value

a square matrix of pairwise F_st values; diagonal has mean heterozygosity within each population as defined by the labels in by

References

PLINK v1.9: https://www.cog-genomics.org/plink2

Purcell S et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81(3): 559-575. doi:10.1086/519795.

Wright S (1931) Evolution in Mendelian populations. Genetics 16: 97-159.

Weir BS & Cockerham CC (1984) Estimating F-statistics for the analysis of population structure. Evolution 38(6): 1358-1370.

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.