data_PoolFreqs: An example pooled allele frequency data set

In j-a-thia/genomalicious: A smorgasbord of R functions for population genomic analyses

An example pooled allele frequency data set

Description

A long-format data table containing individual genotypes for 4 populations, each with 30 individuals, and 200 biallelic SNP loci. Simulated with FastSimCoal2 (Excoffier et al., 2013).

Usage

data(data_PoolFreqs)

Format

A data table with 800 rows and 11 columns.

Details

These columns would be created by genomalicious::poolne_estim_outputs:

• CHROM = The contig ID.

• POS = The SNP position.

• LOCUS = The unique locus ID.

• ALT = The alternate allele.

• REF = The reference allele.

• POOL = The pool ID.

• FREQ = The frequency of the alternate allele.

• DP = The total read depth.

• AO = The alternate read counts.

• RO = The reference read counts.

References

Gautier et al. (2013) Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping. Molecular Ecology, 22(14), 3766–3779.

j-a-thia/genomalicious documentation built on Oct. 19, 2024, 7:51 p.m.