pooldata-class: S4 class to represent a Pool-Seq data set.

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

S4 class to represent a Pool-Seq data set.

Description

S4 class to represent a Pool-Seq data set.

Slots

npools

The number of pools

nsnp

The number of SNPs

refallele.readcount

A matrix (nsnp rows and npools columns) with read count data for the reference allele

readcoverage

A matrix (nsnp rows and npools columns) with overall read coverage

snp.info

A data frame (nsnp rows and 4 columns) detailing for each SNP, the chromosome (or scaffold), the position, Reference allele name and Alternate allele name (if available)

poolsizes

A vector of length npools with the corresponding haploid pool sizes

poolnames

A vector of length npools with the corresponding haploid pool names

See Also

To generate pooldata object, see vcf2pooldata, popsync2pooldata, genobaypass2pooldata and genoselestim2pooldata

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