pooldata.subset {poolfstat} | R Documentation |
Create a subset of the pooldata object that contains Pool-Seq data
pooldata.subset(pooldata, pool.index = c(1, 2), min.cov.per.pool = -1, max.cov.per.pool = 1e+06, min.maf = -1)
pooldata |
A pooldata object containing Pool-Seq information |
pool.index |
Indexes of the pools (at least two), that should be selected to create the new pooldata object |
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) |
A pooldata object with 7 elements:
"refallele.readcount": a matrix with nsnp rows and npools columns containing read counts for the reference allele (chosen arbitrarily) in each pool
"readcoverage": a matrix with nsnp rows and npools columns containing read coverage in each pool
"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 in the reference assembly (3rd column); the allele taken as reference in the refallele matrix.readcount matrix (4th column); and the alternative allele (5th column)
"poolsizes": a vector of length npools containing the haploid pool sizes
"poolnames": a vector of length npools containing the names of the pools
"nsnp": a scalar corresponding to the number of SNPs
"npools": a scalar corresponding to the number of pools
To generate pooldata object, see vcf2pooldata
, popsync2pooldata
make.example.files(writing.dir=tempdir()) pooldata=popsync2pooldata(sync.file=paste0(tempdir(),"/ex.sync.gz"),poolsizes=rep(50,15)) pooldata.subset=pooldata.subset(pooldata,pool.index=c(1,2))