Population allele counts — as_popcounts • corridoR

Every genetic statistic in corridoR works from allele counts per population and locus. A popcounts object holds them: a list with one integer matrix per locus (populations in rows, alleles in columns), plus the population names and the number of individuals sampled in each.

Usage

as_popcounts(x, ...)

# S3 method for class 'popcounts'
as_popcounts(x, ...)

# S3 method for class 'genind'
as_popcounts(x, pop = NULL, ...)

# S3 method for class 'genpop'
as_popcounts(x, ...)

# S3 method for class 'genlight'
as_popcounts(x, pop = NULL, ...)

# S3 method for class 'vcfR'
as_popcounts(x, pop = NULL, ...)

Arguments

x: An object to convert.
...: Not used.
pop: Population of each individual, for objects that do not carry it (a vcfR object, or a genlight without pop). See read_genotypes() for the accepted forms.

Value

An object of class popcounts.

Details

as_popcounts() converts objects from other packages: genind, genpop and genlight from adegenet and vcfR from vcfR. To read a file directly, use read_genotypes().

Examples

ex <- corridor_example()
pc <- read_genotypes(ex$files$small)
pc
#> <popcounts> 6 populations, 100 loci (1-2 alleles per locus)
#>   individuals per population: 8-8
#>   populations: M03_01, M15_01, M28_01, M41_01, M55_01, M70_01