compute.pairwiseFST {poolfstat}

Compute pairwise population population FST matrix (and possibly all pairwise SNP-specific FST)

Description

Compute pairwise population population FST matrix (and possibly all pairwise SNP-specific FST)

Usage

compute.pairwiseFST(
  x,
  method = "Anova",
  min.cov.per.pool = -1,
  max.cov.per.pool = 1e+06,
  min.indgeno.per.pop = -1,
  min.maf = -1,
  output.snp.values = FALSE,
  nsnp.per.bjack.block = 0,
  verbose = TRUE
)

Arguments

x

A pooldata object containing Pool-Seq information or a countdata object containing allele count 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)

min.cov.per.pool

For Pool-Seq data (i.e., pooldata objects) only: minimal allowed read count (per pool). If at least one pool is not covered by at least min.cov.perpool reads, the position is discarded in the corresponding pairwise comparisons

max.cov.per.pool

For Pool-Seq data (i.e., pooldata objects) only: maximal allowed read count (per pool). If at least one pool is covered by more than min.cov.perpool reads, the position is discarded in the corresponding pairwise comparisons.

min.indgeno.per.pop

For allele count data (i.e., countdata objects) only: minimal number of overall counts required in each population. If at least one pop is not genotyped for at least min.indgeno.per.pop (haploid) individual, the position is discarded

min.maf

Minimal allowed Minor Allele Frequency (computed from the ratio overal read counts for the reference allele over the read coverage) in the pairwise comparisons.

output.snp.values

If TRUE, provide SNP-specific pairwise FST for each comparisons (may lead to a huge result object if the number of pools and/or SNPs is large)

nsnp.per.bjack.block

Number of consecutive SNPs within a block for block-jackknife (default=0, i.e., no block-jackknife sampling)

verbose

If TRUE extra information is printed on the terminal

Value

An object of class pairwisefst (see help(pairwisefst) for details)

See Also

To generate pooldata object, see vcf2pooldata, popsync2pooldata,genobaypass2pooldata or genoselestim2pooldata. To generate coundata object, see genobaypass2countdata or genotreemix2countdata.

Examples

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