pooldata2genobaypass: Convert a pooldata object into BayPass input files.

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

Convert a pooldata object into BayPass input files.

Description

Convert a pooldata object into BayPass allele read count and haploid pool size files. A file containing SNP details is also printed out. Options to generate sub-samples (e.g., for large number of SNPs) are also available.

Usage

pooldata2genobaypass(
  pooldata,
  writing.dir = getwd(),
  prefix = "",
  subsamplesize = -1,
  subsamplingmethod = "thinning"
)

Arguments

pooldata	A pooldata object containing Pool-Seq information (see vcf2pooldata and popsync2pooldata)
writing.dir	Directory where to create the files (e.g., set writing.dir=getwd() to copy in the current working directory)
prefix	Prefix used for output file names
subsamplesize	Size of the sub-samples. If <=1 (default), all the SNPs are considered in the output
subsamplingmethod	If sub-sampling is activated (argument subsamplesize), define the method used for subsampling that might be either i) "random" (A single data set consisting of randmly chosen SNPs is generated) or ii) "thinning", sub-samples are generated by taking SNPs one every nsub=floor(nsnp/subsamplesize) in the order of the map (a suffix ".subn" is added to each sub-sample files where n varies from 1 to nsub).

Value

Files containing allele count (in BayPass format), haploid pool size (in BayPass format), and SNP details (as in the snp.info matrix from the pooldata object)

See Also

To generate pooldata object, see vcf2pooldata, popsync2pooldata

Examples

 make.example.files(writing.dir=tempdir())
 pooldata=popsync2pooldata(sync.file=paste0(tempdir(),"/ex.sync.gz"),poolsizes=rep(50,15))
 pooldata2genobaypass(pooldata=pooldata,writing.dir=tempdir())

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