poolfstat (version 2.2.0)

computeFST: 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
)

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

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

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)