pooldata2genobaypass {poolfstat} | R Documentation |
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 |
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())