strataG (version 2.0.2)

structure: 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 = nlevels(strata(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, ...)
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 structure.write.

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".

file

name of the output file from STRUCTURE.

pops

vector of population labels to be used in place of numbers in STRUCTURE file.

Value

structure.run

a list where each element is a list with results from structure.read and a vector of the filenames used

structure.write

a vector of the filenames used by STRUCTURE

structure.read

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

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)
# }
# NOT RUN {
# }