computeFST {poolfstat} | R Documentation |
Compute FST from Pool-Seq data
computeFST(pooldata, method = "Anova", snp.index = NA)
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) |
A list with the four following elements:
"FST": a scalar corresponding to the estimate the global FST
"snp.FST": a vector containing estimates of SNP-specific FST
"snp.Q1": a vector containing estimates of the overall within pop. SNP-specific probability of identity
"snp.Q2": a vector containing estimates of the overall between pop. SNP-specific probability of identity
To generate pooldata object, see vcf2pooldata
, popsync2pooldata
make.example.files(writing.dir=tempdir()) pooldata=popsync2pooldata(sync.file=paste0(tempdir(),"/ex.sync.gz"),poolsizes=rep(50,15)) res.fst=computeFST(pooldata)