computeFST: Compute FST from Pool-Seq data or Count data

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

Compute FST from Pool-Seq data or Count data

Description

Compute FST from Pool-Seq data or Count data

Usage

computeFST(
  x,
  method = "Anova",
  nsnp.per.bjack.block = 0,
  sliding.window.size = 0,
  verbose = TRUE
)

Arguments

x	A pooldata object containing Pool-Seq information or countdata object containing allele counts information
method	Either "Anova" (default method as described in Hivert et al (2018, eq. 9) for pool-seq data and Weir (1996, eq. 5.2) for count data) or "Identity" (relying on unbiased estimators of Probability of Identity within and across pairs of pools/populations)
nsnp.per.bjack.block	Number of consecutive SNPs within a block for block-jackknife (default=0, i.e., no block-jackknife sampling)
sliding.window.size	Number of consecutive SNPs within a window for multi-locus computation of Fst over sliding window with half-window size step (default=0, i.e., no sliding-window scan)
verbose	If TRUE extra information is printed on the terminal

Value

A list with the four following elements:

1. "FST": a scalar corresponding to the estimate of the genome-wide FST over all the populations

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

5. "mean.fst" (if nsnp.per.bjack.block>0): genome-wide Fst estimate as the mean over block-jackknife samples (may slight differ from "FST" estimate since it is only computed on SNPs eligible for Block-Jackknife)

6. "se.fst" (if nsnp.per.bjack.block>0): standard-error of the genome-wide Fst estimate computed block-jackknife samples

7. "fst.bjack.samples" (if nsnp.per.bjack.block>0): a vector containing estimates of the overall between pop. SNP-specific probability of identity

8. "sliding.windows.fst" (if sliding.window.size>0): a 4-columns data frame containing information on multi-locus Fst computed for sliding windows of SNPs over the whole genome with i) column with the chromosome/contig of origin of each window; ii) the mid-position of each window; iii) the cumulated mid-position of each window (to facilitate further plotting); and iv) the estimated multi-locus Fst

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.fst=computeFST(pooldata)

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