allele_frequencies: Compute allele frequencies per markers and populations

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Compute allele frequencies per markers and populations

Description

Compute allele frequencies per markers and populations. Used internally in radiator 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 radiator tidy_genomic_data.
verbose	(optional, logical) verbose = TRUE to be chatty during execution. Default: verbose = TRUE.
parallel.core	(optional) The number of core used for parallel execution during import. 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(s)

Thierry Gosselin [e-mail]

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.