gl.run.structure: Runs a STRUCTURE analysis using a genlight object

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

Runs a STRUCTURE analysis using a genlight object

Description

This function takes a genlight object and runs a STRUCTURE analysis based on functions from strataG

Usage

gl.run.structure(
  x,
  ...,
  exec = ".",
  plot.out = TRUE,
  plot_theme = theme_dartR(),
  save2tmp = FALSE,
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP data [required].
...	Parameters to specify the STRUCTURE run (check structureRun within strataG. for more details). Parameters are passed to the structureRun function. For example you need to set the k.range and the type of model you would like to run (noadmix, locprior) etc. If those parameter names do not tell you anything, please make sure you familiarize with the STRUCTURE program (Pritchard 2000).
exec	Full path and name+extension where the structure executable is located. E.g. 'c:/structure/structure.exe' under Windows. For Mac and Linux it might be something like './structure/structure' if the executable is in a subfolder 'structure' in your home directory [default working directory "."].
plot.out	Create an Evanno plot once finished. Be aware k.range needs to be at least three different k steps [default TRUE].
plot_theme	Theme for the plot. See details for options [default theme_dartR()].
save2tmp	If TRUE, saves any ggplots and listings to the session temporary directory (tempdir) [default FALSE].
verbose	Set verbosity for this function (though structure output cannot be switched off currently) [default NULL]

Details

The function is basically a convenient wrapper around the beautiful strataG function structureRun (Archer et al. 2016). For a detailed description please refer to this package (see references below). To make use of this function you need to download STRUCTURE for you system (non GUI version) from here STRUCTURE.

Format note

For this function to work, make sure that individual and population names have no spaces. To substitute spaces by underscores you could use the R function gsub as below.

popNames(gl) <- gsub(" ","_",popNames(gl))

indNames(gl) <- gsub(" ","_",indNames(gl))

It's also worth noting that Structure truncates individual names at 11 characters. The function will fail if the names of individuals are not unique after truncation. To avoid this possible problem, a number sequence, as shown in the code below, might be used instead of individual names. indNames(gl) <- as.character(1:length(indNames(gl)))

Value

An sr object (structure.result list output). Each list entry is a single structurerun output (there are k.range * num.k.rep number of runs). For example the summary output of the first run can be accessed via sr[[1]]$summary or the q-matrix of the third run via sr[[3]]$q.mat. To conveniently summarise the outputs across runs (clumpp) you need to run gl.plot.structure on the returned sr object. For Evanno plots run gl.evanno on your sr object.

Author(s)

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

References

• Pritchard, J.K., Stephens, M., Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945-959.

• Archer, F. I., Adams, P. E. and Schneiders, B. B. (2016) strataG: An R package for manipulating, summarizing and analysing population genetic data. Mol Ecol Resour. doi:10.1111/1755-0998.12559

Examples

## Not run: 
#bc <- bandicoot.gl[,1:100]
#sr <- gl.run.structure(bc, k.range = 2:5, num.k.rep = 3, 
# exec = './structure.exe')
#ev <- gl.evanno(sr)
#ev
#qmat <- gl.plot.structure(sr, K=3)
#head(qmat)
#gl.map.structure(qmat, bc, scalex=1, scaley=0.5)

## End(Not run)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.