countdata2genobaypass: Convert a countdata 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 countdata object into BayPass input files.

Description

Convert a countdata object into BayPass allele count file. 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

countdata2genobaypass(
  countdata,
  writing.dir = getwd(),
  prefix = "",
  subsamplesize = -1,
  subsamplingmethod = "thinning"
)

Arguments

countdata	A countdata object
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) and SNP details (as in the snp.info matrix from the countdata object)

See Also

To generate countdata object, see genotreemix2countdata, genobaypass2countdata

Examples

 make.example.files(writing.dir=tempdir())
 pooldata=popsync2pooldata(sync.file=paste0(tempdir(),"/ex.sync.gz"),poolsizes=rep(50,15))
 ##NOTE: This example is just for the sake of illustration as it amounts to
 ##interpret read count as allele count which must not be done in practice!
 countdata=genobaypass2countdata(genobaypass.file=paste0(tempdir(),"/genobaypass")) 
 countdata2genobaypass(countdata=countdata,writing.dir=tempdir())

poolfstat documentation built on April 4, 2025, 1:49 a.m.