genepop_colony: Convert Genepop to Colony format.

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

Convert Genepop to Colony format.

Description

Function to convert Genepop to Colony format.

Usage

genepop_colony(genepop, where.plink, where.pgdspider,
  denote.missing = "000", allocate.pgd.ram = 1, path)

Arguments

genepop	the genepop data to be manipulated. This is read in as a complete file path. This will the standard genepop format with a the first n+1 rows corresponding the the n loci names, or a single comma deliminated row of loci names followed by the locus data. Populations are separated by "Pop". Each individual ID is linked to the locus data by " , " (space,space space) and is read in as as a single row (character).
where.plink	A file path to the PLINK installation folder.
where.pgdspider	A file path to the PGDspider installation folder.
denote.missing	The value that denotes missing data in your input file
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.
path	file path to directory where the Colony files (4) will be saved.

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