compute.fstats: Estimate the F-statistics (F2, F3, F3star, F4, Dstat) and...

In poolfstat: Computing f-Statistics and Building Admixture Graphs Based on Allele Count or Pool-Seq Read Count Data

Estimate the F-statistics (F2, F3, F3star, F4, Dstat) and within and across population diversity

Description

Estimate the F-statistics (F2, F3, F3star, F4, Dstat) and within and across population diversity

Usage

compute.fstats(
  x,
  nsnp.per.bjack.block = 0,
  computeDstat = FALSE,
  computeF3 = TRUE,
  computeF4 = TRUE,
  output.pairwise.fst = TRUE,
  output.pairwise.div = TRUE,
  computeQmat = TRUE,
  return.F2.blockjackknife.samples = FALSE,
  return.F4.blockjackknife.samples = FALSE,
  verbose = TRUE
)

Arguments

x	A pooldata object containing Pool-Seq information or a countdata object containing allele count information
nsnp.per.bjack.block	Number of consecutive SNPs within a block for block-jackknife (default=0, i.e., no block-jackknife sampling)
computeDstat	If TRUE compute Dstatistics (i.e. scaled F4). This may add some non negligible computation time if the number of population is large (n>15)
computeF3	If TRUE (default) compute all F3 and all F3star (i.e. scaled F3).
computeF4	If TRUE (default) compute all F4.
output.pairwise.fst	If TRUE (default), output the npopxnpop matrix of pairwise-population Fst estimates (corresponding to the "Identity" method implemented in compute.pairwiseFST) in the pairwise.fst slot of the fstats output object (see help(fstats) for details) that may be visualized with e.g. heatmap function or used with a clustering function (e.g., hclust).
output.pairwise.div	If TRUE (default), output the npopxnpop matrix of pairwise-population divergence (1-Q2) estimates in the pairwise.div slot of the fstats output object (see help(fstats) for details) that may be visualized with e.g. heatmap function or used with a clustering function (e.g., hclust).
computeQmat	If TRUE, compute the error covariance matrix between all F3 and F2 statistics (needed for admixture graph construction). This matrix may be very large if the number of pops is large. It is recommended to estimate it on a reduced sample of pops.
return.F2.blockjackknife.samples	If TRUE (and nsnp.per.bjack.block>0) return an array of dimension (npopxnpopxnblocks) in an admixtools2 compatible format
return.F4.blockjackknife.samples	Deprecated options (since v. 2.2.0)
verbose	If TRUE extra information is printed on the terminal

Details

The function estimates for the n populations (or pools) represented in the input object x:

1. The F2 statistics for all the n(n-1)/2 pairs of populations (or pools) and their scaled version (equivalent, but faster, than Fst estimated with compute.pairwiseFST when method="Identity")

2. If n>2, The F3 statistics for all the npools(npools-1)(npools-2)/2 possible triplets of populations (or pools) and their scaled version (named F3star after Patterson et al., 2012)

3. If n>3, The F4 statistics and the D-statistics (a scaled version of the F4) for all the npools(npools-1)(npools-2)*(npools-3)/8 possible quadruplets of populations

4. The estimated within population heterozygosities (=1-Q1)

5. The estimated divergence for each pair of populations (=1-Q2)

Value

An object of class fstats (see help(fstats) 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))
 res.fstats=compute.fstats(pooldata)

poolfstat documentation built on Sept. 8, 2023, 5:49 p.m.