gl.report.ld: Calculates pairwise population based Linkage Disequilibrium...

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Calculates pairwise population based Linkage Disequilibrium across all loci using the specified number of cores

Description

This function is implemented in a parallel fashion to speed up the process. There is also the ability to restart the function if crashed by specifying the chunk file names or restarting the function exactly in the same way as in the first run. This is implemented because sometimes, due to connectivity loss between cores, the function may crash half way. Before running the function, it is advisable to use the function gl.filter.allna to remove loci with all missing data.

Usage

gl.report.ld(
  x,
  name = NULL,
  save = TRUE,
  outpath = tempdir(),
  nchunks = 2,
  ncores = 1,
  chunkname = NULL,
  probar = FALSE,
  verbose = NULL
)

Arguments

x	A genlight or genind object created (genlight objects are internally converted via gl2gi to genind) [required].
name	Character string for rdata file. If not given genind object name is used [default NULL].
save	Switch if results are saved in a file [default TRUE].
outpath	Folder where chunks and results are saved (if save=TRUE) [default tempdir()].
nchunks	How many subchunks will be used (the less the faster, but if the routine crashes more bits are lost) [default 2].
ncores	How many cores should be used [default 1].
chunkname	The name of the chunks for saving [default NULL].
probar	if TRUE, a progress bar is displayed for long loops [default = TRUE].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Value

Returns calculation of pairwise LD across all loci between subpopulations. This functions uses if specified many cores on your computer to speed up. And if save is used can restart (if save=TRUE is used) with the same command starting where it crashed. The final output is a data frame that holds all statistics of pairwise LD between loci. (See ?LD in package genetics for details).

Author(s)

Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

dartR documentation built on June 8, 2023, 6:48 a.m.