genepop_toploci: Creates a panel of the top n unlinked loci, and exports the...

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

Creates a panel of the top n unlinked loci, and exports the list of loci

Description

Extract the genotypes of individuals at the top n (by Fst) unlinked loci. The default threshold of r2>0.2 is employed for assigning 'linked' loci (default for plink).

Usage

genepop_toploci(genepop, where.plink, where.pgdspider,
  r2.threshold = 0.2, fst.threshold = 0.05, ld.window = NULL,
  ldpop = "All", allocate.pgd.ram = 1, return.workspace = TRUE,
  save.output = FALSE)

Arguments

genepop	A file path to the genepop format file you wish to create your panel from
where.plink	A file path to the PLINK installation folder.
where.pgdspider	A file path to the PGDspider installation folder.
r2.threshold	The minimum r^2 threshold to consider a pair of loci to be in LD
fst.threshold	The minimum FST threshold required to retain a locus
ld.window	Number of adjacent SNPs to compare each SNP against for LD - default is NULL, which translates to a window size of 99999, which essentially asks to compare each SNP against all others
ldpop	A string which populations (default: "All") will be used to calculate linkage disequilibrium. Names must match names returned by genepop_detective().
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.
return.workspace	(default: TRUE) Logical query to return the output to the workspace
save.output	Logical query (default: FALSE) to save the output to the same location as the file being analyzed. Each of the outputs of the function will be saved as a separate file with the file name of the orginal data appended with "_Linkages", "Loci_FST", and "Unlinked_Loci_FST" for the pairwise linked loci along with their r^2, all loci with their global Fst, and only the top unlinked loci with their Fst respectively.

rystanley/genepopedit documentation built on June 14, 2024, 5:34 p.m.