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Compute allele frequencies per markers and populations

Source: R/allele_frequencies.R
allele_frequencies.Rd

Compute allele frequencies per markers and populations. Used internally in radr and might be of interest for users.

Usage

allele_frequencies(
  data,
  verbose = TRUE,
  parallel.core = parallel::detectCores() - 1
)

Arguments

data

A tidy data frame object in the global environment or a tidy data frame in wide or long format in the working directory. How to get a tidy data frame ? Look into genometranslator tidy_genome.

verbose

(optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = TRUE.

parallel.core

Number of workers available for parallel operations. Default: parallel.core = parallel::detectCores() - 1.

Value

A list with allele frequencies in a data frame in long and wide format, and a matrix. Local (pop) and global minor allele frequency (MAF) is also computed.

Author

Thierry Gosselin thierrygosselin@icloud.com