computeFST {poolfstat}R Documentation

Compute FST from Pool-Seq data

Description

Compute FST from Pool-Seq data

Usage

computeFST(pooldata, method = "Anova", snp.index = NA)

Arguments

pooldata

A pooldata object containing Pool-Seq information

method

Either "Anova" (default method as described in the manuscript) or "Identity" (relies on an alternative modeling consisting in estimating unbiased Probability of Identity within and across pairs of pools)

snp.index

A list of SNP to be considered in the computation (by default all the SNP are considered)

Value

A list with the four following elements:

  1. "FST": a scalar corresponding to the estimate the global FST

  2. "snp.FST": a vector containing estimates of SNP-specific FST

  3. "snp.Q1": a vector containing estimates of the overall within pop. SNP-specific probability of identity

  4. "snp.Q2": a vector containing estimates of the overall between pop. SNP-specific probability of identity

See Also

To generate pooldata object, see vcf2pooldata, popsync2pooldata

Examples

 make.example.files(writing.dir=tempdir())
 pooldata=popsync2pooldata(sync.file=paste0(tempdir(),"/ex.sync.gz"),poolsizes=rep(50,15))
 res.fst=computeFST(pooldata)

[Package poolfstat version 1.1.1 Index]