structure: STRUCTURE

In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

STRUCTURE

Description

Run STRUCTURE to assess group membership of samples.

Usage

structureRun(
  g,
  k.range = NULL,
  num.k.rep = 1,
  label = NULL,
  delete.files = TRUE,
  exec = "structure",
  ...
)

structureWrite(
  g,
  label = NULL,
  maxpops = getNumStrata(g),
  burnin = 1000,
  numreps = 1000,
  noadmix = TRUE,
  freqscorr = FALSE,
  randomize = TRUE,
  seed = 0,
  pop.prior = NULL,
  locpriorinit = 1,
  maxlocprior = 20,
  gensback = 2,
  migrprior = 0.05,
  pfrompopflagonly = TRUE,
  popflag = NULL,
  inferalpha = FALSE,
  alpha = 1,
  unifprioralpha = TRUE,
  alphamax = 20,
  alphapriora = 0.05,
  alphapriorb = 0.001,
  ...
)

structureRead(file, pops = NULL)

Arguments

g	a gtypes object.
k.range	vector of values to for maxpop in multiple runs. If set to NULL, a single STRUCTURE run is conducted with maxpops groups. If specified, do not also specify maxpops.
num.k.rep	number of replicates for each value in k.range.
label	label to use for input and output files
delete.files	logical. Delete all files when STRUCTURE is finished?
exec	name of executable for STRUCTURE. Defaults to "structure".
...	arguments to be passed to structureWrite.
maxpops	number of groups.
burnin	number of iterations for MCMC burnin.
numreps	number of MCMC replicates.
noadmix	logical. No admixture?
freqscorr	logical. Correlated frequencies?
randomize	randomize.
seed	set random seed.
pop.prior	a character specifying which population prior model to use: "locprior" or "usepopinfo".
locpriorinit	parameterizes locprior parameter r - how informative the populations are. Only used when pop.prior = "locprior".
maxlocprior	specifies range of locprior parameter r. Only used when pop.prior = "locprior".
gensback	integer defining the number of generations back to test for immigrant ancestry. Only used when pop.prior = "usepopinfo".
migrprior	numeric between 0 and 1 listing migration prior. Only used when pop.prior = "usepopinfo".
pfrompopflagonly	logical. update allele frequencies from individuals specified by popflag. Only used when pop.prior = "usepopinfo".
popflag	a vector of integers (0, 1) or logicals identifiying whether or not to use strata information. Only used when pop.prior = "usepopinfo".
inferalpha	logical. Infer the value of the model parameter # from the data; otherwise is fixed at the value alpha which is chosen by the user. This option is ignored under the NOADMIX model. Small alpha implies that most individuals are essentially from one population or another, while alpha > 1 implies that most individuals are admixed.)
alpha	Dirichlet parameter for degree of admixture. This is the initial value if inferalpha = TRUE.
unifprioralpha	logical. Assume a uniform prior for alpha which runs between 0 and alphamax. This model seems to work fine; the alternative model (when unfprioralpha = 0) is to take alpha as having a Gamma prior, with mean alphapriora × alphapriorb, and variance alphapriora × alphapriorb^2.
alphamax	maximum for uniform prior on alpha when unifprioralpha = TRUE.
alphapriora, alphapriorb	parameters of Gamma prior on alpha when unifprioralpha = FALSE.
file	name of the output file from STRUCTURE.
pops	vector of population labels to be used in place of numbers in STRUCTURE file.

Value

structureRun

a list where each element is a list with results from structureRead and a vector of the filenames used

structureWrite

a vector of the filenames used by STRUCTURE

structureRead

a list containing:

summary

new locus name, which is a combination of loci in group

q.mat

data.frame of assignment probabilities for each id

prior.anc

list of prior ancestry estimates for each individual where population priors were used

files

vector of input and output files used by STRUCTURE

label

label for the run

Note

STRUCTURE is not included with strataG and must be downloaded separately. Additionally, it must be installed such that it can be run from the command line in the current working directory. See the vignette for external.programs for installation instructions.

Author(s)

Eric Archer [e-mail]

References

Pritchard, J.K., M. Stephens, P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
http://web.stanford.edu/group/pritchardlab/structure.html

See Also

structurePlot, evanno, clumpp

Examples

## Not run: 
data(msats.g)

# Run STRUCTURE
sr <- structureRun(msats.g, k.range = 1:4, num.k.rep = 10)

# Calculate Evanno metrics
evno <- evanno(sr)
evno

# Run CLUMPP to combine runs for K = 2
q.mat <- clumpp(sr, k = 3)
q.mat

# Plot CLUMPP results
structurePlot(q.mat)

## End(Not run)

EricArcher/strataG documentation built on May 17, 2024, 12:41 p.m.