genepop_clean: Fixes common formatting problems using PGDspider.

In rystanley/genepopedit: Simple and flexible manipulation of genomic data

Fixes common formatting problems using PGDspider.

Description

Use PGDspider to impliment the proper delimiters in your genepop file.

Usage

genepop_clean(genepop, where.pgdspider, allocate.pgd.ram = 1,
  sample_delim = TRUE, population_suffix = FALSE,
  pop_sample_delim = FALSE, path)

Arguments

genepop	A file path to the genepop format file you wish to create your panel from
where.pgdspider	A file path to the PGDspider installation folder.
allocate.pgd.ram	An integer value in GB to specify the maximum amount of RAM to allocate to PGDspider. The default is 1 GB, which should be sufficient for most analyses.
sample_delim	A logical variable (default = TRUE) that defines whether the function needs to fix the sampleID loci delimiter using PGDspider. Here all files require (space,space scpace) to delimit the sampleIDs from the loci
population_suffix	A logical variable (default = FALSE) that defines whether the function needs to add a population specific suffix to each population. This is required for some genepopedit functionality. Between each "pop" label a Pop(n)_ suffix will be added to each sampleID of genepop.
pop_sample_delim	A logical variable (default = FALSE) that defines whether the function needs to add separation ("_") between population name and sample number. Note if population suffix = TRUE this option is redundant and not executed.
path	the filepath and filename of output.#' @rdname genepop_toploci

rystanley/genepopedit documentation built on June 27, 2023, 11:33 p.m.