genepop_treemix: Convert a Genepop to input required for phython processing to...

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

Convert a Genepop to input required for phython processing to TREEMIX.

Description

Convert Genepop to within-clusters binary PED file for TREEMIX.

Usage

genepop_treemix(genepop, where.pgdspider, where.plink,
  allocate.pgd.ram = 1, keep_inter = FALSE, path)

Arguments

genepop	the genepop data to be manipulated. This can be either a file path or a dataframe read in with tab separation, header=FALSE , quote="", and stringsAsFactors=FALSE. This will be the standard genepop format with the first n+1 rows corresponding to the n loci names, or a single comma delimited 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.pgdspider	A file path to the PGDspider installation folder.
where.plink	A file path to the PLINK 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.
keep_inter	A logical condition statement (default : FALSE) specifying whether to keep the map, ped, and clustering files generated during the conversion.
path	file path to directory where the gzipped Treemix input file will be saved.

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