genoselestim2pooldata {poolfstat}

Convert SelEstim read count input files into a pooldata object

Description

Convert SelEstim read count input files into a pooldata object

Usage

genoselestim2pooldata(
  genoselestim.file = "",
  poolnames = NA,
  min.cov.per.pool = -1,
  max.cov.per.pool = 1e+06,
  min.maf = -1,
  nlines.per.readblock = 1e+06,
  verbose = TRUE
)

Arguments

genoselestim.file

The name (or a path) of the SelEstim read count file (see the SelEstim manual https://www1.montpellier.inrae.fr/CBGP/software/selestim/)

poolnames

A character vector with the names of pool

min.cov.per.pool

Minimal allowed read count (per pool). If at least one pool is not covered by at least min.cov.perpool reads, the position is discarded

max.cov.per.pool

Maximal allowed read count (per pool). If at least one pool is covered by more than min.cov.perpool reads, the position is discarded

min.maf

Minimal allowed Minor Allele Frequency (computed from the ratio overal read counts for the reference allele over the read coverage)

nlines.per.readblock

Number of Lines read simultaneously. Should be adapted to the available RAM.

verbose

If TRUE extra information is printed on the terminal

Value

A pooldata object containing 7 elements:

1. "refallele.readcount": a matrix with nsnp rows and npools columns containing read counts for the reference allele (chosen arbitrarily) in each pool

2. "readcoverage": a matrix with nsnp rows and npools columns containing read coverage in each pool

3. "snp.info": a matrix with nsnp rows and four columns containing respectively the contig (or chromosome) name (1st column) and position (2nd column) of the SNP; the allele taken as reference in the refallele.readcount matrix (3rd column); and the alternative allele (4th column)

4. "poolsizes": a vector of length npools containing the haploid pool sizes

5. "poolnames": a vector of length npools containing the names of the pools

6. "nsnp": a scalar corresponding to the number of SNPs

7. "npools": a scalar corresponding to the number of pools

Examples

 make.example.files(writing.dir=tempdir())
 pooldata=popsync2pooldata(sync.file=paste0(tempdir(),"/ex.sync.gz"),poolsizes=rep(50,15))
 pooldata2genoselestim(pooldata=pooldata,writing.dir=tempdir())
 pooldata=genoselestim2pooldata(genoselestim.file=paste0(tempdir(),"/genoselestim"))